And DS9, which introduced the concept, concluded they were the bad guys and that S31 made things worse on the whole. The dark and gritty Trek that deconstructs the franchise as a whole and the Federation in particular still decided that Section 31 was a bad idea.
On top of that, every show after DS9 completely fails to understand that S31 was supposed to be a conspiracy, not an actual branch of Starfleet. The bit of the charter they cite to justify themselves requires some pretty significant mental gymnastics to make work, and it most certainly doesn’t literally sketch out a whole branch of Starfleet. It’s clearly there for things like when you have to violate time travel laws to pick up whales from the past to keep Earth from getting blown up, or when you have to direct a universe destroying anomaly to a specific universe so that your transporter duplicate can fix it before it destroys other universes. Those are extraordinary threats. The stuff S31 typically concerns itself with, like Romulans scheming against everyone, are ordinary threats that regulations already cover.
It’s also arguably something that Article 14, Section 31 is actually meant for. The Dominion was in the process of conquering the entire quadrant and dismantling the Federation government, among others, and they had the means and manpower to do so. That’s an extreme and existential threat. The thing Sloan tricked Bashir into doing with the Romulans, on the other hand, is just a regular Tuesday with the RSE as your neighbors and therefor not an extreme threat.