That's the really sad thing about Trek Lit. They took this very interesting organization, which had its pros and cons, and just turned it into this strawman evil organization that's only rivaled by Mass Effect's Cerberus in stupidly evil actions.
There was never anything the least bit ambiguous about Section 31. They were quite unambiguously the bad guys from Day One in the canon, and Treklit just reflects that. (There is nothing "pro" about an organization that routinely appoints itself judge, jury, and executioner, and which engages in mass murder and genocide.)
You want moral ambiguity? Treklit's take on Starfleet Intelligence is very morally ambiguous.
I can think of plenty of pros and cons to Section 31's existence.
-No one knows or believes they exist, giving them all sorts of leeway to advance the Federation's best interests without dealing with the sometimes incompetent Federation leadership or negatively harming the Federation's reputation by being officially connected to the organization
-Small cells of individuals are able to undertake operations that have serious ramifications in interstellar politics with a minimum of collateral damage, leading to greater benefits in the long term
-Rigorous selection requirements ensure that individuals recruited into the organization are loyal to the Federation and principled enough to use the minimum force necessary
-All agents are highly skilled and well trained, meaning that if one goes rogue, he or she might cause a lot of damage
-By the nature of their job, they have to engage in ethically questionable things that might violate some of the ideals of the Federation
-Are convenient scapegoats for all sorts of bad things the rest of the Federation because of their methods and pragmatism
When it comes down to it, I consider the guys who decided that genocide was the only way to decapitate the leadership of an empire with genocide and atrocity happy fascists to be the good guys because in the long run, they would've kept the other guys from killing even more people in their quest to bring "order" to the galaxy. Would it have been great if Section 31 hadn't needed to deploy the disease? Sure. But that only would've been possible had the Founders not been the massive dicks that they were.
I see no reason to arbitrarily label people who go with the most logical and pragmatic solution to a problem as evil. Nor do I see any logic in extrapolating that Section 31 is responsible for so much evil and retarded shit that TrekLit has conjured up just because they came up with a bioweapon to kill the 99% of the Changelings responsible for every evil thing the Dominion has done ever.