Well, not to get too far off topic, but the Justice League has similar standing with its government(s) as S31. No authorization for its existence, no chain of command related to government authority, and no responsibility to the populace or the government. But they're "good guys" and S31 isn't? Is it the lack of government-backed legitimacy that is bad, or is it the actions taken that are bad?
Batman's a vigilante like Sloan. What's the real difference between them? Their actions.
Actually I think the Justice League has some standing with the government as they usually have some liaison they work with.
And on the Batman thing he needs the trust of the police to be as effective as he is, if he ever steps out of line and loses that well he loses that effectiveness because he has to dodge the cops while still trying to fight crime.
Plus Batman is around becuase of how ineffective the usual cops are Section 31 doesn't have the justification becuase nothing they do couldn't be done by Starfleet or Starfleet Intelligence. Hell most of the time 31 needs Starfleet personal to do things so their really superfluous.
Of course ultimately I think the difference is that Star Trek is meant to be more realistic than a comic book world (hint hint Trek lit writers and editors)