Would Section 31 ever really fall? Wouldn't some concerned idiot just start it up again?
Heck, I think that's the only way it's managed to exist as long as it has. The idea of a vast conspiracy staying secret for generations is as fanciful as psychic powers or time travel, a fictional conceit or paranoid delusion that doesn't wash in the real world. The larger a conspiracy gets, the more lines of communication it has that can be intercepted and the more opportunities there are for its members to make mistakes that will compromise its secrecy. And the more people it has, the more likely it is that some of them will have second thoughts and decide to reveal what they know. And it couldn't last generations without new people coming in and replacing the old, and who's to say they'd share their predecessors' views or commitments? Sooner or later, something's got to give. Not to mention that in a democratic state with a free press, there are going to be a lot of people who have a vested interest in uprooting secrets and corruption, whether it's journalists seeking to make a name for themselves or politicians seeking to discredit their rivals.