Honestly, it's worse than "there needs to be a space CIA."
Because even without Section 31, the Federation still has Starfleet Security and Starfleet Intelligence. They still have police and spies. Those police and spies still have to make the hard choices; still might have to swim in morally murky waters, where there are no good choices, and it's just about finding the least bad choice.
But Starfleet Security and Starfleet Intelligence are accountable to people. They have oversite. When they make those hard choices, they have to write a report explaining them and justifying them, and if their justification is rejected, there are consequences.
Section 31 isn't "the people who operate in the gray area and make the hard choices." Section 31 are the people who do whatever the fuck they want, and tell themselves they're making the hard choices, but it's always other people who suffer for those choices.
And it is very significant that Section 31 was first introduced in DS9, because DS9 are the people who live in the grey area; the ones far away from paradise that things aren't always easy, and that sometimes have to make the hard choices.
And one of the themes DS9 plays with is that being the Federation doesn't automatically make you right. Assuming you're in the right because you're the good guys tends to lead to very bad things.
Over a year before Section 31 was introduced, there had already been a two-parter about how, if you give up all your values in the name of security, you're the bad guys. And then Section 31 is introduced in an episode where they look at a guy who is already a hero many times over, who has risked his life multiple times and saved countless lives, and who spent months in a brutal prison camp only last year, and decide to kidnap and psychologically torture him. They then get away with this.
They are not the good guys. They are not a "necessary evil." They are a continuation of the idea of people doing bad things and claiming it's for the greater good, and how that's a bad thing.
Because we have a word for a culture where everyone believes their the good guys and has a wonderful life, but it's only able to exist because of a group doing terrible things without oversite.
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