The problem though is that Section 31 isn't a evil organzation in the sense that they want to do evil things out of cruelity or rule the world. There is enough shades of grey to their motives to make them fit within the boundries of Trek sensibilities. All you really need to sell them is a character that is sympathetic to degree like Sloan. If people like a character they will forgive just about any sins when it comes to fiction IMO. If your Section 31 agents are carboard villians then it might feel wierd but carboard villians will destroy any type of villians you use.
Jason
Evil/not evil, I think their big thing is not maintaining transparency (to use a recent overused political word). They're shadowy and sneaky, but then I'm reminded of Picard's huge and pretty damning lecture to Wesley about how Starfleet represents the pursuit of truth.