Also, when it comes to interstellar politics, things that are in the best interests of the organization (peace with the Romulans, a diminished Dominion threat) tend to be in the best interests of the people as well.
Section 31 acts in its own best interest. Nothing else. They claim to serve the Federation, but if they did that, then by definition they would answer TO the Federation. They don't do that. They quite literally do whatever they want.
An organization can't be acting in the best interests of any people or government if it doesn't hold itself accountable to that same people or government.