I think fans also forget that Starfleet has it's own normal intelligence agency. Section 31 gets tossed in way too much. Sloan has told us that it operates outside of Starfleet to protect the Federation's best interests. I would surmise that it would only take on operations it deems to be the upmost threat to the Federation. Not just any old run of the mill intelligence op. That's not the impression of Section 31 that I get.
I think their also confusing Section 31 with Mass Effect's Cerberus who lets face are a lot better at the amoral covert splinter cell with no accountibility thing the 31 is.