I don't buy the idea that Section 31 isn't sanctioned by the Federation in some way.
It possible that they aren't authorized by the entirety of the Federation governance, as to whether they're supported by
civilians in the Federation (and how many) is a different question.
I think it likely that individuals in the Federation, and in Starfleet, support S31. Finance, equipment, transportation, access. Somewhere there were the people and facilities that created the sickness that the Founders were infected with.
If everything that S31 did during the Dominion War was reveled, what percentage of the Federation populace would ultimately agree with their intended goals, if not their methods?
If you usurp the jurisdiction of the executive you are a criminal organisation
And if the executive is just sitting on it's hands while a powerful enemy advances and maneuvers it's assets into position, what then?
"Oh, we all should wait for the executive to act (someday)."
If S31 hasn't this authorisation, they are formally a gang of murderers and terrorists.
And the actions seen in the episode In The Pale Moonllight, would you describe the DS9 senior officers (and Garak) as "a gang of murderers and terrorists?"
Just as you would if S31 did
the exact same thing?
Powers of life and death are solely within the gift of the executive to delegate
So the Federation you envision is one where people are not allowed to protect themselves?
None of that is comparable to an organization which attempts genocide or builds top secret scary evil starships.
In terms of a basic concept it is comparable, it's individuals stepping forward and doing something without first seeking permission. They are protecting their families (Sloan spoke of his family), protecting their community, and protecting the Federation as a whole.