I think Sisko was just pissed (and I don't mean drunk

) at Dukat for beating him up. I am sure once he had time to cool down his judgment was more balanced.
And Speaking of evil: I am not sure what to call a man that drops deadly poison on a planet where there are children, just to secure the capture of one man.
I call him human. Humans are capable of great good and reprehensible evil. While I can't stand Sisko's actions, he at least provided warning and the Maquis were able to evacuate. That is more than could ever be said of Dukat.
The thing about DS9 is that they rarely played it safe. Sisko made morally questionable decisions, but so did Starfleet. The aspects of the impact of the cold war, and eventually hot war, with the Dominion led to some pretty nasty behaviors.
As much as I like the optimism of the Federation, there has to be challenge to those ideals, or they mean very little.
I know DS9 had its ups and downs, but it was interesting, to me, to see the charactesr go through them.