The theme of DS9 was moral ambiguity, and a darker tone to events.... particularly with Garaks sinister and shady nature, which ends up saving the Federation, despite his conflicted motives.
Dukat, after all, stressed how Bajor only triumphed due to his restraint, but how he was both vilified by Sisko while being punished by Cardassia, and this conflict drove him to seek Siskos approval, but still Sisko judged him to the end.
And of course there was the finale of Section 31 supposedly engaging in genocide against the Founders, despite that biological warfare was their specialty in the Gamma Quadrant, while they were also the aggressors in the war with the Federation... and the Dominion only needed to surrender and negotiate for a cure.
So because the writers lacked the skill to resolve conflict peacefully as in TOS, they made a whole series war out of it.