Dukat's ability to "negotiate" for all of Cardassia to join the Dominion really wierded me out. At the point at which he announced Cardassia's entry to the Dominion, he had lost his standing with the legitimate civilian government and his rank of Legate because of his daughter Ziyal. What I'm guessing took place was the same thing that Weyoun tried to pull with Sisko, offering absolute rule of his government. The fact that Dukat had ties with the military that helped him gain support is irrelevant to the feelings of the Cardassian populace at large, and specifically the civilian government. The Dominion probably just swept in with their first big fleet, headed straight to Cardassia Prime, quickly and quietly disposed of the civilian government, and stuck Dukat in power as their puppet dictator, with the Central Command sitting on it's hindquarters all the while.
I guess the point I'm trying to make here is that the civilian populace, and possibly some of the military, shouldn't be vilified as much as many seem keen to do. The Cardies were in no way ever unified in their desire to join the Dominion, and in fact most of them probably did not have a choice in the matter. Therefore, Cardassia shouldn't be completely dissolved as a nation-state, but rather allowed to reinstate it's original government and go from there. I also agree with those that said the Obsidian Order would have to go, and I humbly submit that the Central Command (or what was left of it) should be tossed as well, since they were most likely complicit in the coup d'etat.
Granted, it may have been necessary to secede some of the former Cardassian territories to the victors, especially those that had already substantial military assets placed on them. I'm pretty sure the Klingons would insist on it, and probably the Romulans if any of the territories were already close to home (since we know how much the Rommies like to play their cards close to the chest
). Cardassia itself would probably have to be left alone, for the simple reason that it's their homeworld and they need that to rebuild their civilization (if it wasn't too badly decimated by the Dominion already, another thing that's kind of left up in the air).