I still don't get the impression that S31 being legitimate was the writer's intention at the time. That Sloan is or was from Starfleet Intelligence and uses Starfleet resources while Starfleet Command looks the other way also works for interpreting his statement. Starfleet Command refusing to confirm or deny S31's existence can be used to back up basically any position. For instance, if S31 is a conspiracy within Starfleet, then Command can't acknowledge it or they would have to do something about it; acting like they don't know anything means they can keep letting S31 do what they want.

Even the bit of the charter mentioned in ENT implies that Harris and S31 are taking a very liberal interpretation of the Starfleet Charter. "Reread the Charter, Article 14, Section 31. There are a few lines that make allowances for bending the rules during times of extraordinary threat." But S31 operates day-to-day against ordinary and mundane threats, like everyday Romulan politics. And that bit doesn't seem to mandate the creation of a special branch just for extreme threats. Rather, it seems like it's there to cover the random crazy things that Starfleet crews run into once every few years, like taking a BoP back in time to gather some whales not resulting in punishment because of the extreme threat posed by the whale probe, even though they blatantly violated a bunch of rules regarding time travel.