Mage and I think the cover up would do more damage than that actually assassination. If someone else knows, if some else leaks the info the fallout would be much worse. Once it is known that both Starfleet and the Cardassian government hid the truth, all heck would break loose.
Well, that's the question, isn't it? Setting aside the question of how this will impact Cardassian politics -- because, remember, Ganar resigned because she realized that Starfleet Intelligence would eventually find out she had learned from the CIB that a True Way member may have done it, but failed to alert the Federation government of CIB's suspicions [in part because she did not want to admit that she could not control CIB] -- let's consider things from a Federation-centric perspective.
Starfleet hiding the truth? Setting aside the semantic question of whether or not two people -- Picard and Akaar -- can be said to represent all of Starfleet as an institution... Consider what they know:
They know the CIB thinks the True Way did it. They know that Garak thinks the True Way did it. They know that Ganar thought the True Way did it, and resigned to avoid the wrath of a Federation government angry that she didn't immediately tell them she thinks a True Way member did it.
What they don't
have is actual evidence
that the True Way did it. They have a suspicion -- a suspicion they harbor, in essence, because they trust the judgment of Elim Garak. They have a suspicion that they did not share with the President Pro Tempore in part because of lack of evidence -- which is a reasonable reason -- and in part because they don't trust Ishan to have a reasonable, proportional reaction. They are worried that a disproportionate reaction from Ishan will lead to a sundering of the UFP/CU alliance, and therefore to the Khitomer powers being weakened before the Typhon Pact.
Now, is that a "cover-up?" I'm not sure. I'd call it a cover-up if they had actual evidence... but they don't. In essence, all they have is the word of Elim Garak.
By the same token, there's an argument to be made that this sort of suspicion shouldn't be hidden from the civilian leadership just because the military disapproves of them. On the other hand -- you gotta ask yourself if it's responsible to report to the President every conspiracy theory your field men hold -- and Picard is a field man, at the end of the day. I don't know. But I'd be surprised if there weren't suspicions like that held in real life by military officers that aren't reported to their civilian governments for lack of evidence.
And I think Themet was just a poorly done caricature by Miss. McCormack. I waiting for him to twirl his mustache and tie a widow to train tracks. And the most interesting thing was that Cardassia First actually had some very valid concerns.
Nothing about Themet struck me as unrealistic. He seemed like a very typical nationalist, of the sort you find in all societies. Nationalists like him thrive on exploiting legitimate concerns for the benefit of their extremist, authoritarian agendas. [E.g., Tea Party fanatics complaining about legit problems with Obamacare, or Golden Dawn in Greece complaining about E.U.-imposed austerity measures.] Heck, Cardassia First was literally named after a real organization
[albeit one whose members were mostly more moderate or more liberal than its most famous spokesman
The government signing a secret agreement with the Federation, which the people can not see until after it has been signed.
I'm sorry, but this complaint is complete bullshit. This is how all
treaties in real life are negotiated; you can't hash out agreements between sovereign states in a public committee room, because then nothing can get done.
What happens from there is, they're signed... and then they have to go to their states' respective legislatures for ratification! And that's when the public gets to review the specific treaty document, and pressure their democratically-elected legislators to either support or oppose the treaty draft, just like any other bill. The treaty is not binding law until -- no, unless
-- the democratically-elected legislature ratifies it.
Meanwhile -- yeah, the exact document wasn't yet available for public view, but the relevant details were all leaked to the public well before the treaty went to the Cardassian Assembly and Federation Council. It's not like this was classified secret -- it was negotiated in private for practical matters, for later public veto or ratification, but it wasn't a state secret that subjected the leakers to potential prosecution.
And besides -- the negative aspects of the treaty were ones Garak convinced the Feds to change.
Cardassia allowing the Federation to dictate policy. Even though the war is long over, a new government is in charge, and Cardassia is an ally of the Federation. I don't think the US is still telling Germany, Japan, and Italy how to run things.
Other posters have already pointed out that the U.S. was running the show in its occupied WW2-era enemies for far longer than the UFP has been dominating Cardassia. Indeed, handing over day-to-day autonomy to a new local democracy just one year after the war [as seen in A Stitch in Time
and Cardassia: The Lotus Flower
] and restoring full sovereignty only ten years after the war is positively fast-paced compared to the punishment we exacted from Germany.
But I'd just like to point out that you're kidding yourself if you think the German, Italian, or Japanese governments don't still reply to a U.S. command to jump by asking, "How high?"