"Section 31" was probably inspired by La Femme Nikita's "Section One" organization, which is used to perform extra-legal operations against terrorists. The beauty of that show was that the protagonist, Nikita, knew about S1's past, what it was capable of, but stayed with the organization in order to steer it towards the right direction. In a Star Trek setting, a show centering around S31 could have the characters tackle morally-grey scenarios, both from within and outside of Federation influence. Certainly, you could have your classic spy thriller elements, where S31 has the deal with the likes of the Orion Syndicate, the Tal Shiar, the Obsidian Order, those parasites from the TNG "Conspiracy", mad scientists, rogue admirals, etc. Their mission? To help the Federation maintain the appearance of "paradise".
Food for thought.