Well, that's getting into major retcon territory, IMO. Not that you couldn't tell an interesting story with that premise, but if Starfleet is secretly rotten to the core, it's not really a Star Trek story any more, is it?
Well all of those corrupt admirals have to be coming from somewhere, and Section 31 shouldn't still exist if it is "rogue" AND known about by the "normal" SF members. I would believe that there is a black ops/CIA/NSA type division in the shadows, absolutely.
It doesn't change the "trek" future; it gives a plot structure to explore morality, gray areas, good of the many (federation) vs the few (acceptable casualties to Section 31).