IMO the writers who created the section 31 storyline seemed to have something to say about the cia, and they intended it to temper people's rah-rah notions about starfleet. the idea of a whole interstellar federated government with only benevolent motives is hard to swallow even as science fiction

There's some argument to be made that Section 31 is a semi-autonomous group that most of Starfleet doesn't know about and the ones who do are afraid of, also that by the DS9 era it might literally be one guy