I'm not quite sure what the discussion is about. It's obvious that Section 31 was supposed to exist as stated, complete with awesome powers.
The story logic gives credit for victory in the Dominion War to Section 31 even while some scenes also suggests that Odo and Sisko's "sacrifice" were responsible for victory. Similarly the story logic and the oft-repeated theme about saints in paradise determined that Section 31's methods were a necessity (possibly tragic,) while some scenes showed a few of the more idealistic characters held that they were excesses that should be stopped...after
this particular mission, of course.
There isn't sufficient detail, despite all those hours of episodes, to decide the issues associated wtih Section 31 by objective (in-universe, at least) facts. This is intentional, I'd say, a way of dodging the issue. You can present your characters as people who don't think their villains and give them their say. Neither the show nor the viewers are required to accept their rationalizations, only their humanity in clinging to them. That is, if you accept that their is such a thing as objective truth, which quite a few don't.
Since there's nothing really valid to say about the issue in the series' terms, we can only compare things to the real world. Some people believe that empire is good, that the natural state of humanity is war and therefore that Section 31 is fundamentally a good. (Again, possibly tragic according to the sentimentality of their personal tastes.)
My take is that empire is not a good, much less a necessity. Nor do I accept that the human condition is war.
Further, the absurd powers attributed to Section 31 falsely equate acceptance of both these reactionary propositions with a choice between life and death. One of the prime functions of civilization is to give us collectively the power to live without internecine violence. In the real world, the contributions of intelligence agencies is highly debatable. And the contribution of covert ops (which is what Section 31 really does,) is entirely negative. Covert ops are
war, and war is no longer a necessity, but a crime.