Sisko did take Eddington's betrayal too personally and as a bruise to his ego but I don't think he stepped over the line. And Eddington's delusions of picaresque grandeur were really just as bad and way more creepy.
Let's also remember that nobody died when Sisko gassed the planet, and he was completely sure Eddington would continue to do it to Cardassian planets.
You honestly think that a planet with thousands, if not millions of people, can be evacuated by a terrorist group that doesn't even have enough ships to fight their enemies in an open battle in the window of an hour? We couldn't even evacuate New Orleans with a week's foreknowledge of Katrina.