I write ST fan fiction with a group of others and we have differed from the books in several major ways, with a major plot in several stories being the war between Section 31 and its numerous pawns and counter-31 cabals, and TBH it quite often just devolves into screw ups on all sides. We have devised a plan to cut the head off the S31's snake which will come to fruition if we get that far ahead in our stories, but I for one am fed up of them in the stories we're writing. Like David Mack
is writing the denouement of the MU saga, I would like to see someone write the denouement of Section 31.
I agree that no secret organization can exist forever, and ordinary fiction is replete with examples of said organizations being ousted. An upcoming one is from Robert Ludlum's estate with his Covert One series. While the characters are trying to stop the latest biological atrocity from taking place, they're distracted by a Washington beltway group trying to discover the truth behind Covert One and destroy it, presumably in an effort to bring down the President, who is the only person that Covert One answer to.
In this instance, Covert One is an agency comprised of individuals who do not know each other but each answer to the head of the agency who then answers to the President, though several operatives may work on the same mission from different angles. They're not out to protect themselves, but to protect the American people from biological warfare.
I have no doubt that there are such groups out there, in addition to the alphabet soup of law enforcement agencies, because sometimes you need to fight dirty and if you have complete oversight you can't do that. But I'm not a conspiracy nut like Ludlum was in his later years, or like Clive Cussler seems to be in his books, with Dirk Pitt uncovering a single person at the head of a conspiracy in every novel.