I don't think it's all that clear. If Section 31 are "just bad people," then so is Starfleet. The Admiral in "Improbable Cause" was hoping the Cardassians would be successful in wiping out the founders. Starfleet command authorized Sisko to defraud the Romulan government to drag them into a war that would cost them millions, and condoned everything that happened in the operation. Admiral Ross, the alleged "Goodmiral" helped Section 31 put a terrible Romulan in power, because he secretly worked for Starfleet. Bashir deduces that dozens and dozens of people at Starfleet medical had to have been involved to create the virus and give it to Odo.
If DS9 has shown anything, it's that unlike TNG, Federation principles aren't enough to keep the Federation alive. S31, in this show and in ENT, are not depicted as purely "bad people."