A premise for a series that might fit better with Trek's general philosophy would be to have Section 31 as the antagonist and have the protagonist be a group of captains, admirals, members of Starfleet Intelligence, and others that actively opposes Section 31 and seeks to reveal the wicked machinations of the organization to the greater public. If that wouldn't work, perhaps a tv movie which would show the downfall of Section 31 would work better.
Hmm possibility...But every other power in the Alpha Quadrant has their own version of a CIA of sorts.
So does the Federation -- it's called Starfleet Intelligence.
Section 31 is not like the CIA. The CIA is authorized and overseen by the democratically-elected Congress, and takes its orders from the democratically-elected President.
Section 31 is an extra-legal conspiracy within the government that answers to no-one. Think less "Section 31" and more "Mafia."
Funny, in the Dominion Wars, no one questioned the motives, or integrity of Section 31.
Bullshit. The episodes they appeared in featured the main characters questioning their motives and integrity all the time.