^ Innocent people are always displaced and killed in armed conflicts. Not making excuses but the Maquis were a significant risk to peace and stability in that area of the quadrant. Starfleet or the Federation might make the trade off that this event, while devastating to hundreds or thousands of people, is worth the cost of keeping the Cardassians appeased and onside.
Given the devastating power of weapons in the 24th century they might have a different view on WMDs. A single photon torpedo potentially has the power to kill millions and no one blinks at their usage. Maybe there might be an element of that in the 24th century humans or the Federation in general have a slightly different view on "WMDs" and what Sisko did isn't considered all that bad.
Back to the post-Dominion War Cardassia, I don't think we've mentioned the fact that the Dominion handed over several territories to the Breen near the end of the war. You would think after the war the Cardassians would want them back. However, I can't see the Breen giving them back.