First of all, I don't think we're supposed to like Section 31 from an operational standpoint. They clearly operate in a black operations/plausible deniability realm that many real world agencies have, except they usually have both official and classified operations under one roof. Star Trek, like it is want to do, places all the skullduggery under one umbrella term, in which Section 31 is neither confirmed, nor denied, and utilizes its assets as needed.
Now, I do appreciate having Section 31 because it fixes a rather annoying problem in Star Trek that many admirals and leaders are either evil, or prone to conspiracy. That is such an odd look for an organization that allows people remain in a posting as long as they like so long as it works, but as soon as you become upper leadership you grow evil?
That is not encouraging as an organization.
This isn't me saying all bad things done by Starfleet is a Section 31 conspiracy but only that it is nice to have some influence that causes the high rate of bad admirals than just the obsession with being a captain.
Now, I do appreciate having Section 31 because it fixes a rather annoying problem in Star Trek that many admirals and leaders are either evil, or prone to conspiracy. That is such an odd look for an organization that allows people remain in a posting as long as they like so long as it works, but as soon as you become upper leadership you grow evil?

This isn't me saying all bad things done by Starfleet is a Section 31 conspiracy but only that it is nice to have some influence that causes the high rate of bad admirals than just the obsession with being a captain.