^^"The entire crew of DS9" is an exaggeration. The senior staff know about them, but that's like seven people in the entire Federation. Not really enough to expose such a secret.
OK, that's what I meant when I said the "crew." Sorry if I wasn't clear. But what's to stop Sisko and "crew" from going to Starfleet Command and the Federation Council with what they know? Or Jake Sisko from spreading their existence on the Federation News Service?
Well, Sisko did make inquiries about Section 31 and Sloan to Starfleet Command, who stonewalled him.
Presumably Section 31 has ways of siliencing or at least discrediting anyone who tries to go public about them.