It's a fundamental misunderstanding of what Section 31 is supposed to be. Sloan wasn't a good guy. 31 actively tried to commit genocide.
The idea behind them is that arguments of ends justifying the means and "getting dirty" to preserve higher ideals is morally, philosophically, and practically bankrupt. The Federation didn't need 31 to win the war, and in fact, their methods would have made it much worse. Section 31 as a plot device exists to show us that there will always be those looking to use higher ideals to support terrible actions, and we must be constantly vigilant against them.
It truly pains me how that message has been twisted, and people think Section 31 are not only good guys but also cool.
Sorry if I wasn't clear; I didn't mean to make it sound like an attack or a lecture. Section 31 is just one of my pet peeves in Trek for a while. We are in agreement! 😊