Although to be fair when the Federation Council had the cure to the sickness that Section 31 imposed upon the Founder, the Council decided not to simply give it to them, but instead to employ the cure as a bargaining tool to end the war.Going by the show, they're the only group of people in the Federation that's consistently pragmatic, utilitarian, and equipped with foresight.
Good for them.
I would imagine that the vast majority of the people in the Federation don't answer to the President, why would it be different for folks in S31?They don't answer to anyone - not even the president.
