Generally speaking, I'd like to argue that virtually none of the shadow jobs in Star Trek are the doing of Section 31 - not even most of those that S31 claims are its doing.
Outsorcing evil to a bunch of others, to a cigarette-smoking, well-manicured cabal , is both extremely unrealistic and dramatically extremely unsatisfactory. Evil is us. We are the ones who travel the paved road to hell. And some of us like to take credit for doing the paving - but the good intentions of S31 need not really be the ones that result in the evil consequences. Those consequences may come to be without conscious effort on the part of devious masterminds, and indeed usually do.
Yeah but look at the alternative. The writers of Deep Space Nine were looking to inject the morally perfect Federation of The Next Generation with some reality in a way that creatively didn't compromise what had already been established. Thus, with Section 31 we learn that the supposed necessary evils of building and maintaining an empire are done quietly, often with the collusion of Starfleet officers and officials. It's a decent work around in my opinion, at least for a tv show.