It's not that we are judging the need, quality or ethics of or for Section 31, it's what they represent in a gaming environment that is the problem, and the types of play that is associated with them...
As a plotline, Section 31 is a great thing, all of the above ideas are superb. I quite like the idea that Sloan was operating all on his own.. there could well be another 3 or 4 Section 31's operating out there: Pulling strings, gathering information, and getting ready to act on whatever THEIR agenda is. I even like the idea of a single character becoming entangled in Section 31, much as Bashir did: But there's a difference to becoming entangled, burned and stinging, than wholeheartedly avowing to the cause from the beginning. There is a difference between a player working with the GM on a 'cool' story line in which he gets hoodwinked by a Section 31 agent (alleged!), than a player who is constantly stabbing all his peers in the back, and dragging round the story in a direction he wants to go in!
In my old PBEM, one of the first rules of the game was "You cannot create a character who outranks the captain, without his permission" I.e. you can't overrule the GM. Especially in PBEM's in which players are given a lot of freedom to do as they wish, and time to think of clever ways of doing things, that single tennet has to exist, because the 'Captain' is responsible for keeping the game moving, and making sure the story works and makes sense. Introducing Section 31 is basically a way of subverting this, not only in play but in intent: It is a statement of intent deliniating: "I want to be able to set my own agenda and not have anyone tell me what to do." This would not be acceptable in a paper and pencil game any more than it would on a PBEM!