I see there is disagreement over whether the CU was a match for Starfleet. I thought based on on-screen evidence (such as the fact that
Galor-class ships were seldom a match for Starfleet's, that the Maquis could make such effective hit-and-run strikes,
and that the Klingons, who are arguably Starfleet's equal, went in an completely wiped out Cardassia.) Though the examples I cited could all be refuted; I won't bother to do it right now.

As for non on-screen evidence, I thought the quasi-official stats demonstrated that Cardassian tech, population, and resources lagged behind that of the other Powers. Wasn't that why they went to exploit nearby, defenseless Bajor? I don't recall ever hearing about them fighting real wars against significant opponents, except for the recent border skirmishes during the on-again, off-again, UFP-CU conflict.
As for Sisko not being punished: I'm not sure I agree that he didn't put the colonists in absolutely
no danger. He did not give a very long warning. What if some people had been out far from a settlement on a hike, or foraging, or undergoing surgery, etc.? I guess they could be beamed up, but was Sisko
sure there were enough transports and that everyone could be safely evacuated? I don't think Sisko and Eddington are morally equivalent. Eddington was an avowed terrorist; Sisko was a Starfleet officer. I'm not trying to argue who's in the right here, Starfleet or the Maquis (I still don't know).
What I find surprising, however, is that Starfleet allowed Sisko to take unilateral action that rendered an inhabited planet lethal to all humans. I'd think Starfleet would not tolerate that sort of action. Maybe in Archer's or Kirk's era, but not in the late 24th century. And this is the same Starfleet that agreed to completely stop all cloaking research just to satisfy the Romulans, even though it seem the Romulans weren't in the position to be making that kind of demand at the time. Recall how later Sisko and Ross were in no mood to celebrate the destruction of Cardassia, even though the CU was responsible for initiating the costly and bloody war. Sisko also felt horrible about the death of a Romulan senator, a criminal, and a few others in
In the Pale Moonlight, even though it was essential for winning the war. I'm not saying whether Sisko was being prudent/correct in taking the biogenic action, just that I can't believe he wasn't reprimanded by Starfleet, or that it didn't later bother Sisko's conscience. I suppose he figured that by taking that action he severely disrupted Maquis activity by forcing the surrender of Eddington, and the Maquis, right or wrong,
were a huge sticking point between the UFP and the CU. He probably figured he was ultimately saving many lives at a low risk. But still....
I'm also not sure I agree that it was the Maquis that were principally -- or even partially -- responsible for Dukat inviting the Dominion to Cardassia. I thought he did it because Cardassia had been devastated by the Klingons, and that only a side effect of that was that the Maquis were essentially left alone and had a free reign in the DMZ --
not that they threatened CU territory proper enough to incite Dukat to join the Dominion. ?