Actually, it is the suffix -on that causes the secondary stress to happen in most situations, like when it is added after a consonant.
This phenomenon is very common in AmE. But not the case in BrE: OBED and many other British dictionaries show otherwise (no secondary stress). [ Though many British physicists still stress the word in a way that gives secondary stress on the second syllable.]
OE suggests that "on" made its first appearance in the early 19th century in atomic physics:
ion (n.) 1834 [interestedly I've heard people pronounce it two ways: ˈaɪən and ˈaɪˌɑn]
introduced by English physicist and chemist Michael Faraday (suggested by the Rev.
William Whewell, English polymath), coined from Greek ion, neuter prp. of ienai "go,"
from PIE root *ei- "to go, to walk".
So called because ions move toward the electrode of opposite charge.
It was not until the late 19th century that it is used as a suffix.
In 1894, Stoney coined the term electron to describe these elementary
charges, saying, "... an estimate was made of the actual amount of
this most remarkable fundamental unit of electricity, for which I have
since ventured to suggest the name electron". The word electron is
a combination of the word electric(icity) and the Greek suffix "tron",
meaning roughly 'the means by which it is done'. The suffix -on which
is now used to designate other subatomic particles, such as a proton
or neutron, is in turn derived from electron.
In the 20th century, it becomes a fashion to use it for coining new terms not only in physics:
proton is coined in 1920 {it was used earlier in embryology (1893) at a translation of German anlage},
neutron [ˈn(j)uˌtrɑn] is coined in 1921,
photon (a particle-like package of light) is coined in 1926,
positron [ˈpɑzəˌtrɑn] (the antiparticle of electron) is coined in 1933,
negatron [ˈnɛɡəˌtrɑn] (the antiparticle of proton) is coined around 1933,
fermion [ˈfɜrmiˌɑn] (any particle that follows the Pauli exclusion principle)
and
boson [ˈboʊsˌɑn] (any particles that don't follow the exclusion principle)
are coined in the mid 20th century
[A famous example of boson would be the higgs boson which may help us to gain a
deeper insight into dark matter and dark energy, recently discovered by CERN
(though it is not exactly the higgs boson predicted by the Standard Model)]
lepton (any particle that does not undergo strong interactions but follows the exclusion principle E.g. electron) is coined in 1948
muon [ˈmjuˌɑn] (an unstable, negatively charged lepton) is coined in the mid 20th century
gluon [ˈgluˌɑn'] (an exchange particle responsible for strong interaction) is coined in the mid 20th century
but also in other branches of science:
interferon
[ˌɪntərˈfirˌɑn] Biochemistry
a protein released by animal cells, usually in response to the entry of a virus, that has >the property of inhibiting virus replication.
1957, coined in English, so called because it "interferes" with the
reduplication of viruses. From interfere + subatomic particle suffix
-on.
codon
[ˈkoʊˌdɑn] Biochemistry
a sequence of three nucleotides that together form a unit of genetic code in a DNA or RNA >molecule.
1962, from code (n.) + -on.
operon
[ˈɑpəˌrɑn] Biology
a unit made up of linked genes that is thought to regulate other genes responsible for >protein synthesis.
1960s: from French opérer ‘to effect, work’ + -on.
radon
[ˈreɪˌdɑn] Chemistry
the chemical element of atomic number 86, a rare radioactive gas belonging to the noble gas series.
*1918, from radium (q.v.) + -on suffix of inert gases. *
A very famous physicist, Richard Feynman, even used the prefix -on to make up his own word, "parton" when he explained a seemingly-complex concept. And thus you can tell at that time the prefix -on was pretty well-used in the science community.
Notes: Not all 19th & 20th century scientific terms ending with "on" make use of the prefix "-on". One example would be ion as mentioned above, and here is another example
neuron [ˈn(j)ʊˌrɑn]
"a nerve cell with appendages," 1891,
from German Neuron,
from Greek neuron (see neuro-). Used earlier (1884) for "the spinal
cord and brain."
Both the suffix -on and terms that exhibit secondary stress, such as neuron, ion, come from Greeks words.
So you are right, the Greeks are behind this.