Section 31 was a terrible idea just to make the Star Trek universe more "dark" and leave the optimistic future behind.
If by "dark" you mean realistic, then I agree.
I didn't find Section 31 realistic, I found it absurd that a regular bureaucratic organization like Starfleet, that already had special operations divisions and Starfleet Intelligence, would need a group that was so secret that no one even knew of its existence.
military, or quasi-military organizations just don't work that way. In the Romulan Empire, folks know of the existence of the Tal Shiar. In the Cardassian Empire, folks know of the Obsidian Order.
the stuff we see Sec. 31 doing would be the same stuff Starfleet Intelligence could be doing. They didn't need to introduce some new comic book-esque group into the Trekverse.
That was exactly the point I was trying to make earlier. Section 31 is redundant at best; we already have Starfleet Intelligence that does what Section 31 is purported to do. All Section 31 is good for is making the Federation "darker and edgier" and we already had rogue admirals that served that purpose (to much greater effect in my opinion).
Section 31 is just some writer's poor attempt at creating a Federation equivalent of the Tal'Shiar or the Obsidian Order. What makes this a poor attempt is that S31 is so secret that apparently not even the Federation government is aware of its existence! This makes Section 31 look like the paranoid, deluded extremist cabal they truly are.
If you're trying to make the Federation more morally dubious, don't make some secret unsanctioned conspiracy that no one knows about and try to peg the Federation government as morally equivalent to the Romulans or Cardassians.