Section 31 is not the CIA or the KGB. Those are state-sanctioned intelligence agencies operating under the supervision of their governments. I'll never understand why people keep making the mistake of using that analogy. Section 31 is not an intelligence agency. Starfleet Intelligence is the Federation equivalent of the CIA. Section 31 is a rogue organization operating outside the law and answering to no one. Maybe at the beginning, their intentions were good, but after 200 years with no accountability, the only things they truly protect are their own interests and their own secrecy. They have no allegiance to anything but their own power. They may use the security of the Federation as their excuse for wielding that power in defiance of law and morality, but make no mistake, they are closer to the Mafia than the CIA. They are a force of corruption by their very nature.
Funny story, Christopher, I ran a Section 31-themed Star Trek (Decipher) RPG campaign. I was going with the idea that they were morally ambiguous and their actions were arguably justified to save the lives of the many rather than the morals of the few.
And as the campaign progressed, they STILL came off as major [insert Klingon vulgarities].
I believe moral ambiguity and Star Trek is a natural fit, ironically, because hard moral choices should go hand in hand with its idealism. Section 31, when written well (like here), best contrasts against Starfleet Intelligence (which I'd love to see a series about). The criminal and self-justifying versus the noble.
As it was said in my campaign (completely spontaneously):
NPC: Section 31 is a patriotic organization, a militia if you will, which believes the Federation's ideals are dangerously misguided and prone to appeasement rather than securing the security of the Federation. They operate clandestine missions of their own accord while working behind the scenes to prepare the way for a stronger more effective government.
PC: So they're terrorists.
NPC: We don't work against the Federation and often work as deniable assets.
PC: Useful terrorists.