Background in gizli devlet and derin devlet
Turkish gizli devlet, translated into English 'secret state',
foreshadows and overlaps with Turkish derin devlet, 'deep state'. The
former shows up as early as 20 Oct 1955 in the title of a pamphlet:
The delegation asked the authorities to confiscate four anti-Jewish
publications which recently appeared on the stands here. One of them is
the "Secret State and Program of Conspiracy" by Cevat Rifat Atilhan, a
notorious anti-Semte [sic].
That translation of gizli devlet shows up again in the title of a
1957 pamphlet by the same author in 1970 (The National Union Catalog
1956 through 1967):
Gizli Devlet ve porgrami The secret state Istanbul?
The (check-out with free account) 1999 Warrant for genocide: key elements of Turko-Armenian
conflict (Dadrian, Vahakn N), cites a 1996 book by Suat Parlar, The
Secret State: From Ottoman days to the present.
In this context of gizli devlet, the Turkish 'secret state', alongside
frequent association of the English phrase 'secret state' with state-level
security and intelligence forces, Robert D. Kaplan, a contributing editor
for The Atlantic Monthly (later The Atlantic), details a political
sense of derin devlet, Turkish for 'deep state', in "A different
democracy" (paywalled; 01 Jul 1998, The Boston Globe):
...what Turks call "the deep state", symbolized by the military, hides
behind the white-lie facade of the superficial civilian cabinet.
Kaplan goes on to observe, of the Turkish military, that it
is less a fighting machine than the country's best-organized, most
respected secular institution, with deep historical roots.
Kaplan reports that at the time, the term derin devlet, 'deep state',
was used to describe the military's covert response to these Turkish political events:
In 1996, a democratically elected, hopelessly divided Parliament...led
to a weak minority government of Muslim fundamentalists. ... The Turkish
military...began undermining [the] government through intimidation, press
briefings, and regulations that curtailed the business activities of [the
government's] religious supporters.
Kaplan's is the earliest significant use of 'deep state', the translation
of derin devlet, that I found. It is followed by a fair sprinkling of
other uses:
a (paywalled) 2000 USA newspaper article by Stephen Kinzer, "Pope's
attacker carries secrets home",
"He must know a great deal about the connection of the extreme right
wing to intelligence services, police and other elements of what we
call 'deep state'."
a (check-out) 2001 USA book by Daniel G. Bates, Peoples
and cultures of the Middle East,
In Turkey, for example, peope complain bitterly about the so-called
"deep state" or the perceived collusion among business, military, and
political leaders.
a (paywalled) 2001 British newspaper article by Chris Morris, "Turkey
jails spy and ex-police chief for running hit squad",
...it sparked genuine fears among ordinary Turks that gangs within
the state had been given unfettered control, and could be a threat to
democracy. Suspicion of what Turks call "deep state links" is still
extremely strong.
another (paywalled) 2001 British newspaper article by Chris Morris, "Gang
rule keeps Kurdish lands lawless",
[Diyarkabir's] popular police chief, Gaffir Okkan...was assassinated
in a professional ambush in the city centre.
....
The official explanation is that Okkan was murdered by the radical
Islamic group Turkish Hizbullah. On the streets of Diyarbakir, however,
nearly everyone seems convinced that what they call the "deep state" was
involved.
a (paywalled) 2002 Canadian article by Patrick Graham, "Troubled Turkey goes to polls",
This is part of a turf war between the Islamists and Turkey's
long-established secularists, led by the army, who remain loyal to the
legacy of the country's founder, Kemal Ataturk. The last time an
Islamist government got out of line it was removed by the military in
what analysts call a post-modern coup....
The military, along with judges and the bureaucracy, are the ultimate
arbiters of Turkish life and would prevent Islamic fundamentalism from
taking over Turkey no matter what the cost.
But the legitimacy and reputation of the "deep state," as some call it,
suffered badly in the 1990s....
a 2003 essay by Soli Özel, "Turkey at the polls: After the
tsunami",
At the scandal's heart was the lawless "dirty war" that Turkey's
shadowy "deep state" had been waging in the southeast.
a (paywalled) 2003 British newspaper article by Helen Smith, "New
breed of Islamic politicians start to find their feet",
Mr Erbakan's humiliating removal and the prohibition of his Welfare
party in 1998 apparently convinced the AKP that provoking Turkey's
"deep state" — the military, bureaucracy, media and
judicial circles that make up its ruling
elite — would be political suicide.
a (paywalled) 2003 British newspaper article by Jonny Dymond,
"West must help Turkey fight back",
The rubble had not been cleared from the two synagogues bombed last
weekend when the Briutish consulate was ripped apart and the HSBC
headquarters destroyed.
....
Some theorise that the military-bureaucratic
complex — the "deep state", the government within a
government — had allowed the attacks to happen.
Two uses of 'deep state' in 2004 represent the term in its original Turkish sense. One is a footnote in a USA Naval Postgraduate School thesis by Michael Naoum, "The
Greek-Turkish rapprochement process, 1999-2004: paradigm shift or
EPI-phenomenon",
The forces described by Onis are also known as the "deep state."
The other 2004 use is in a (paywalled) newspaper article, "Struggle for
the soul of Islam":
In Turkey the government and the state are not always synonymous. The state bureaucracy can prove hard to control for even the most adept party in power. And Turkey's so-called deep state, made up of ruling elites from the military, judicial branch, business and media, has long wielded tremendous power behind the scenes.
A 2005 use in a book by Speros Vyronis, The mechanism of
catastrophe: the Turkish pogrom of September 6-7, 1955, and the
destruction of the Greek community of Istanbul, suggests that Turkish
derin devlet is simply a more recent term for what was called gizli
devlet:
Governmental control of Turkey's judicial system involved the bondage
and corruption of the latter, as well as the tradition of the "gizli
devlet," that is, the "hidden state" (or, as it's been called more
recently, the "derin devlet," or "deep state").
Five more uses in 2005 confirm that the sense of the Turkish derin
devlet, 'deep state', encompasses not just intelligence agencies, but
intelligence agencies acting in cahoots with assorted others, including
gangsters, drug dealers, and other government agencies and branches, outside the
rule of law.
In 2006, a book by Peter Galbraith, The end of Iraq: how American incompetence created a war without end mentions the Turkish 'deep state':
Some Turkish strategic thinkers, including those within the so-called "deep state" comprising the military and intelligence establishments, see Iraqi Kurdistan as a potential asset.
Extension beyond Turkey
Ryan Gingeras, in a 04 Feb 2019 article, "How the deep state came to America: A history" (Texas National Security Review) offers an in-depth account of "the history of how and why the phrase entered American parlance." He observes that the "first scholarly effort to internationalize the concept of the deep state came in an essay pubished in 2009 by Norwegian scholar Ola Tunander", but goes on to recount that
Tunander presented this view of the deep state before a conference held in Melbourne in 2006. ... Attending the conference was the scholar perhaps best known for popularizing the concept of "parapolitic," Peter Dale Scott. Up until that point, Scott later explained, he had never heard of the deep state but was taken by Tunander's analysis of Italy and its applicability elsewhere. "I was very gratified," he told me in 2007, to realize "how closely, how very closely, my analysis of America fit Ola Tunander's [thinking] of both America and other states."
The history by Gingeras accurately details when the sense of 'deep state' shifted from its original sense, a straightforward reference to the Turkish concept, to a broader application to other state political systems.
The extension of the term 'deep state' to USA political systems, for example, began to appear in Peter Dale Scott's works, from Tunander's generalized concept, starting in 2007. For example, the term appears several times in a 2007 essay (dated 2004 at archive.org, but internal references date to 2007, so the essay must have been published that year or later), "9/11, JFK, and War: Recurring patterns in America's deep events" (bolding mine; see also quotes in the OP from Scott's 2007 book, The Road to 9/11):
If history is what is recorded, then deep history is the sum
of events which tend to be officially obscured or even suppressed in
traditional books and media. Important deep events include the politicial
assassinations of the 1960s, Watergate, Iran-Contra, and now 9/11. All
these deep events have involved what I call the deep state, that part of
the state which is not publicly accountable, and pursues its goals by
means which will not be approved by a pubic examination. The CIA (with its
on-going relationships to drug-traffickers) is an obvious aspect of the
deep state, but not the ony one, perhaps not even the dirtiest.
When I talk of a deep state, this term (as opposed to
others, like deep politics), is not my own invention. It is a translation
of the Turkish gizli devlet, or derin devlet, a term used to describe
the networks revealed by the so-called Susurluk incident of 1996, when
the victims traveling together in what became a deadly car crash were
identified as "an MP, a police chief, a beauty queen and her lover, a top
Turkish gangster and hitman called Abdullah Catli."
Later uses in the same essay establish that Scott, when referring to the
'deep state', sometimes merely means 'intelligence agencies'. For example, on p 4:
3) Commission recommendations to increase power of intelligence
agencies, or deep state
Scott, however, again makes the connection between the gizli devlet and the deep
state in Turkey on p 21:
The pattern moreover is that exhibited by the gizli devlet or deep
state in Turkey, where a Parliamentary Investigation into the Susuruk
Report concluded that the deep state had used the drug-trafficking Grey
Wolves and fomented conflicts in the 1970s between the Turkish right and
left. The alliance between the deep state and drug traffickers has
surfaced in other countries as well, incuding France, Italy, Mexico,
Panama, Pakistan, Taiwan, and Japan.
Scott, according to his statement in a 2007 podcast interview with Gingeras, credits Tunander with the original broader application of the term 'deep state' beyond Turkish political systems, to USA and other nation's political systems.
Appropriation degenerates the concept
The 2019 Gingeras article in Texas National Security Review points to the amplification beginning in 2008 of the 'deep state' from Scott's 2007 book, The Road to 9/11, as the initial route to popularization of the term:
It was as a result of this book, and the exposure [Scott] received thereafter from Alex Jones and others, that many Americans first entertained the notion that a deep state lorded over the United States.
(The Southern Poverty Law Center describes Alex Jones as "almost certainly the most prolific conspiracy theorist in contemporary America.")
Gingeras notes the fuzziness of the 'deep state' concept:
Yet defining what exactly constitutes a deep state, let alone documenting its existence, is another matter. The story of how the deep state entered American consciousness underscores the inexact science and fancifulness that hampers any discussion of secret states and shadow governments.
....
Since it was first coined over 20 years ago, no precise definition for what it means has fully taken hold. Use of the phrase generally denotes belief in an informal or parallel government that exists to countermand legitimate, usually more democratic, institutions. Who constitutes this shadow government depends widely on whom you ask and where or when the discussion takes place. While the term originated with reference to the hold security institutions have over state and society (such as in Turkey), the list of deep state actors can include social groups accused of exploiting everyday citizens, like the mafia, “big business” or ideological extremists.
Michael Lofgren's use of 'deep state' in his 2014 essay, "Anatomy of the Deep State" represents a re-appropriation of the concept first developed by Tunander, then particularized by Scott, and finally degenerated by Alex Jones and company. Lofgren's belated 2014 appearance in the 'deep state' circus ring, along with the earlier hand-off of US application of the term from a left-aligned scholar to a right-aligned conspiracy theorist, supports and reinforces Gingeras's 2019 conclusions, among them that
More often than not, the search for a deep state provides license for those seeking to conflate and marginalize political dissidents and opponents.