I'm looking for metaphors (non-jocular) with the same meaning as "Trojan Horse" - "A person or thing intended to undermine or destroy from within."
A Wolf in sheep's clothing metaphor may also fit the context.
is an idiom of Biblical origin. It is used of those playing a role contrary to their real character, with whom contact is dangerous. As a fable it has been falsely credited to Aesop and the theme is now numbered 451 in the Perry Index. The confusion has arisen from the similarity of the theme with fables of Aesop concerning wolves that are mistakenly trusted by shepherds; the moral drawn from these is that one's basic nature eventually betrays itself.
Fifth column (Wikipedia) comes to mind.
A fifth column is any group of people who undermine a larger group—such as a nation or a besieged city—from within. The activities of a fifth column can be overt or clandestine. Forces gathered in secret can mobilize openly to assist an external attack. This term is also extended to organized actions by military personnel. Clandestine fifth column activities can involve acts of sabotage, disinformation, or espionage executed within defense lines by secret sympathizers with an external force.
Patrick M added
Critically, however, the Fifth Column idiom originates from supporters or sympathizers for the attackers converted or persuaded to change sides from within the defenders. Almost all usages of Trojan Horse imply an attack originating from outside under disguise.
Emilio Mola, a Nationalist General during the Spanish Civil War, told a journalist in 1936 that as his four columns of troops approached Madrid, a "fifth column" of supporters inside the city would support him and undermine the Republican government from within.
Note also that a column is specifically a military formation, making General Mola's initial metaphor slightly off. These may give the wrong impression of your metaphor to a historically minded or pedantic audience. Nevertheless, Fifth Column has spread widely in usage since its coinage and matches your example meaning of undermine or destroy from within very well.
I would disagree with the definition given in the question. A Trojan Horse is specifically a gift, something given under the guise of friendship intended to destroy your enemy.
Therefore, you could say a poisoned gift or a poison apple.
The term sleeper cell is defined by Oxford Dictionary Online as
A secretive group of spies or terrorist agents that remain inactive within a target population until ordered to act.
Obviously, this is an extreme version of the hidden threat concept, akin to the original Trojan horse. It could be used figuratively to refer to lesser threats than terrorism.
This may also be called a sleeper nest. [Dictionary.com]
Related is the term sleeper agent (or sometimes simply sleeper), also from ODO
A secret agent who remains inactive for a long period while establishing a secure position.
Finally, there is Manchurian candidate, from the Urban Dictionary
a candidate running for office who publicly supports one group to win election, but uses his executive or legislative powers to assist an opposing group; it should not be confused with a sleeper agent who has been brainwashed into working for a political party
This seems focused on politics, as was the movie from which it derives. [IMDB.com]
Reading the answer offered by @itcouldevenbeaboat, several thoughts can to mind, including poisoned apple, worm in the apple and finally nourish a viper in one's bosom. This phrase comes from a fable by Aesop, The Farmer and the Viper. The gist of the story is
A farmer finds a viper freezing in the snow. Taking pity on it, he picks it up and places it within his coat. The viper, revived by the warmth, bites his rescuer, who dies realising that it is his own fault. The story is recorded in both Greek and Latin sources. In the former, the farmer dies reproaching himself 'for pitying a scoundrel', while in the version by Phaedrus the snake says that he bit his benefactor 'to teach the lesson not to expect a reward from the wicked’. [Wikipedia]
A mole is a trusted member of one organization who is secretly employed by another, competing organization to gather intelligence on or even disrupt the operations of the target organization. A double agent is similar.
Poisoned chalice would be an obvious choice, with the bonus of Shakespeare using it in Macbeth.
The term "poisoned chalice" is applied to a thing or situation which appears to be good when it is received or experienced by someone, but then becomes or is found to be bad.
An assignment, award, or honour which is likely to prove a disadvantage or source of problems to the recipient:
inside man or man on the inside describes somebody who appears to be working for them, but is actually working for you.
The expression to white-ant conveys the same sense as Trojan Horse.
The other team attempted to white-ant our proposal.
http://en.wikipedia.org/wiki/White_anting However, the link states that the expression is uniquely Australian. I'm not sure if that's correct.
Another expression to consider is "angel of light" to describe one who appears good but means ill, from a biblical reference:
"And no marvel; for Satan himself is transformed into an angel of light." 2 Corinthians 11:14 King James Version (KJV)
Sting Operation comes to mind: http://en.wikipedia.org/wiki/Sting_operation