So I was thinking of writing some post-DS9 (maybe abut 10-15 years after) fan fiction.
I was thinking about doing something with Section 31but some questions popped up. After Sloan died we were left to wonder is is Section 31 is gone? was it just Sloan?
Lets say it was not just Sloan, if there were other involved and Starfleet officials caught up and apprehended them. Could Section 31 ever be a legit yet still secret agency with in Starfleet?
Does section 31 have to much of a bad history (attempted genocide etc..) for Starfleet to use them in a more controlled manor?
Should Starfleet abolish S31 and try to have some other type of black-ops agency?
Should S31 always remain a more rogue agency that answers to no one in order to protect the Federation?
1. The DS9 relaunch literature establishes that Section 31 is bigger than Sloan and that there are other agents. This is taken up in other Trek Lit. works as well, the best example being the S31 novel mini-series. Supporting the idea that Section 31 is bigger than one man is also their appearance on ENT.
2. With Trek Lit., there are hints that Section 31 will eventually get its comeuppance. I believe that's hinted at in the future sections of the ENT novel, "The Good that Men Do". As to the second half of that question, I think that's something you could explore in your fanfic.
3. Section 31's history is a subjective thing since we really haven't seen any official history besides their involvement in the Klingon augment incident. Trek Lit. made the Omega molecule disaster and the assassination of Gorkon part of a Section 31 plot, but of course that's non canon. So, a lot of their history is mere speculation and ripe for you to fill in the blanks.
4. Abolishing Section 31 is another decision up to you. I know I've seen one fan fic where have a similar organization (though I think it is concurrent with Section 31). If you feel that Section 31 doesn't fit your fan fiction but you want something along that line, why not get rid of them? The section does have haters in the fanfic community, along with supporters, so I don't think getting rid of them will be meet with a lot of anger. Even fans might be interested to see what you're planning with your new group.
5. In my own fanfic, I pretty much do what you're asking in this question. I like S31 and have used them quite a bit. So I would say yes to this question. But once again, you've got to do what's best to fit your story or series.