Section 31 was portrayed as having extraordinary powers so that its methods could be portrayed as being a genuine choice between life and death. Section 31 means life while ideals mean dying for them. The very possibility that living morally is a means to a fuller, happier and longer life is foreclosed as unimaginable. This says more about the writers as people than it does about the human condition.
The retorts above emphasizing the awesome power of the Dominion and the essential identity of all Founders as a single (im)moral agent, the Great Link, merely replicate the same kind of distortion. It would have helped if Star Trek had a greater emphasis on science. Being soft SF, Trek could conceive such absurdities as space war, interstellar empires, programmed loyalty in intelligent beings and so forth. The existential threat posed by the Dominion is Nonsense Taken Seriously. Perhaps getting all solemn and pompous adds to the entertainment value? Hard to imagine but tastes do vary.
But even if so, such foolish premises make the storyline irrelevant as a commentary on the human condition. There is no eternal empire, no monolithic ruling class, no military threat so grave that genocide is both justified and possible. By the way, the importance and relevance of simple physical possibility is sadly underrated. In practice, any storyline playing with genocide is bascially arguing that there is some dreadful enemy in real life against whom "we" must exercise merciless violence, in self defense of course. All the absurd powers imputed to the SF versions are mere expressions of hysteria about the RL foes.
Off hand, the only possible exception I can think of is the extermination of the Ori in Stargate SG-1. Although that series was very pro-military, the extermination of real "gods" also functions as a call for extremely practical atheism!