Dukat is evil, but not evil like in a comic-book world, evil like in the real world. People who commit horrible things might be seemingly nice fellows, they might have a family and genuinely love their children. And like Dukat, evil people try to rationalize their actions and delute themselves.
Just take a look at all the torturers of the previous administration, not the one in boots but the one in suits, the masterminds behind the agenda.
DUKAT: "Of course I hated them! I hated everything about them! Their superstitions and their cries for sympathy, their treachery and their lies, their smug superiority and their stiff-necked obstinacy, their earrings, and their broken, wrinkled noses!"
SISKO: "You should have killed them all, hm?"
DUKAT: "Yes! Yes!! That's right, isn't it?! I knew it. I've always known it. I should've killed every last one of them! I should've turned their planet into a graveyard the likes of which the galaxy had never seen! I should've killed them all."