I think remnants of the now defunct military dictatorship that ran Cardassia for centuries would be resentful of the Federation's presence on Cardassia. It would be naive to assume that people like Gul Madred would do a 180 and would now support the Federation after the war. I could imagine a new version "The True Way" terrorist group, rising up to oppose the Federation's presence on Cardassia. Look at it this way, most modern day Germans hate the Nazis, but still a small minority in Germany who support Nazi ideals. There will always people who embrace destructive ideologies.