Yeah, Sisko's actions in "For the Uniform" was mind-numbingly stupid...thank God everything else about him is awesome, or I'd hate the character.
There is absolutely no justification for a trained military officer to use a WMD against a human colony just to capture one very persistent terrorist. Imagine any real world scenario with the same general concept. The fact that there were no consequences just made it even worse. It would have been interesting if the Maquis at least tried to get revenge on the Federation somehow for such a callous act against fellow Federation citizens, rogue or not.