If they really are rogue then why isn't the Federation stopping them? Hunting them down publicly or at least acknowledging their existence when Bashir complained.
Remember the context. This wasn't the normal state of affairs; this was during the Dominion War, when the Federation was on the run and in danger of defeat. DS9 was often about challenging the Federation's values, exploring the difficulties of remaining true to one's ideals when the situation grew dark enough. "It's easy to be a saint when you live in paradise," as Sisko said in "The Maquis." So it's fundamentally missing the point to think that DS9 was representing how the Federation
routinely does business. The Dominion War arc was about putting the Federation through hell, straining its ideals and morals to the breaking point, and exploring how those ideals became compromised in the process.
So in the depths of the Dominion War, when the Federation was in danger of extinction, Starfleet and the UFP government looked the other way when Section 31 did terrible things, because they felt they had to. That
does not mean they would
always tolerate Section 31. It meant that, when their very survival as a civilization was at stake, they would bend rules that under normal circumstances they would rigorously uphold. It's the same as "In the Pale Moonlight." Just because Sisko tolerated Garak's crimes in that episode, when the situation was desperate enough that he had no choice, that absolutely does not mean that Sisko would
always tolerate murder and deceit. Assuming that would be completely misunderstanding the episode. And assuming that the Federation would
always tolerate Section 31 is misunderstanding the entire Dominion War storyline. It was supposed to represent an extreme, a breaking point, not the normal state of affairs.
(I'm reminded of how people missed the point of Frank Miller's
Batman: The Dark Knight Returns. It was never meant to depict how Batman would normally operate, but to represent the worst possible extreme that Gotham could sink to and explore what extremes Batman would be driven to in response. Yet fans and creators overlooked that and used it as a model for how Batman and Gotham were routinely portrayed for the next decade or two.)