So I always felt that it was a missed oportunity not to make Julian the head of Section 31, taking over from Sloan. He could of shaped it into something more compassionate whilst at the same time being a super cool secret agent like he had always wanted to be.
Nothing was said about Sloan being the head of Section 31. If Bashir did find himself in the role I suspect he'd see about dismantling it in short order, maybe not broadcasting all they've done over the subspace channels but at least bringing it to light for Starfleet.
Sloan wasn't the head of Section 31, he was an agent of it. They could have had a good arc where Bashir tries to take down Section 31, but instead of putting the final nail in the coffin, is convinced that an organization like them is actually necessary but they can do it without all the worst things they do like assassinations.
But it was never said that he wasnt head of section 31..... I would of liked to see him do something exciting like that, trying to repent for the crimes of the agency, prehaps a bit of moral conflict, teaming up with Garak to go on secret missions or using Miles to infiltrate Starfleet academy.
I always saw S31 as never having any sort of structure by the DS9 days. In the 22nd century when Starfleet was formed it did have a director and a management structure, with agents in the field dealing with threats and recruiting others, then training them up for the work that was required, before those new agents went out and did the same and so on, all working under the Section 31 directive though autonomous and not being directed by any one person or command structure. Them being without any sort of oversight or organisation, doing what they feel duty-bound to do to safeguard the Federation, would be a sort of Anti-Starfleet which makes them very "alien" in nature and more unsettling. Bashir's moral core was very set. S31 were wrong in what they did, they had to be brought down, so much so that when given the opportunity he risked his brain dying with Sloan's just to dig up enough dirt on them to do so, which would make the idea of him willingly joining seem a little far fetched.
Spoiler: What We Left Behind Documentary In the documentary, the writing staff has re-gathered to pitch a hypothetical 8th season Premier, and this is an element they discuss.
Certainly Sloan was probably just a supervisory agent of Section 31, and Bashir just targeted him because Bashir knew how to lure him. But Bashir was offended by the entire Section 31, and would take the whole operation down if he could.
Inquisition and Pale Moonlight were the two worst placed episodes ever. In one, it's revealed that Starfleet has it's own "dirty work" organization, in in the next, Sisko does Starfleet's dirty work because he presumes no one else can. Way better would have been to: 1. Flip flop the two. Pale Moonlight comes first. 2. Have Sisko use Bashir as part of his plot to sucker the Romulans in "Pale Moonlight". He and Garak were used to teaming up anyway. Then, S31 sees what Sisko and Bashir did. They're impressed, but Sisko's status as a station commander/religious icon makes him a poor choice. So, they recruit Bashir instead, via "Inquisition".
It would be interesting to see Bashir joining Section 31 and working his way to the top out of a desire to, at first, handicap the organization and ultimately bring it down from the inside, but then some devastating event (perhaps Starfleet Security's failure to discover and prevent the Zhat Vash-supported synth attack on Mars?) forces him to keep it going and, probably naively, try to at least steer it in a new, less Orwellian direction. I feel like that might be more in keeping with DS9's tone.
Unfortunately, any big organization (like the United Federation of Planets) needs an organization like S31. That is to say, an organization that gets dirty when it needs to. If Bashir crushed S31, it would simply reconstitute itself.
In the novels, at some point Julian and Sarina go undercover for Starfleet Intelligence and join 31 to find a way to destroy it from the inside. Unfortunately, they learn that Control, the nameless head of S31 is a super-AI, created during the time NX-01 was being build and Starfleet was formed. It was aware enough to know that S31 could never be 100% hidden, people would find out. So every now and then, it would set events in motion to let 31 be destroyed, and it would rebuild it from scratch. It saw a possibility in Julian and Sarina to do just that; expose 31 to the public, completely, and become something completely different as a Super AI. It let to Sarina's death and Julian now being completely catatonic and in a wheelchair. Castellan Garak, the leader of the Cardassian Union, took him into his care. Julian now 'exists' completely withdrawn into himself, responding to nothing and no one. The entire idea of Control as we see it in Discovery was based in part on that. Although with many differences as well.
Come to think about it, that's one scene I'd have loved to see. Garak's reaction to either Bashir or Sisko when he hears of the existence of Section 31.
My idea of S31 as it was only in DS9 was kind of like how you think about Oceania and Big Brother in 1984, in that there's never a concrete thing we know about it and that's the point. There could be a thousand operatives or it's just Sloan and some guys in a lab cooking up a disease. It's all lies or half-truths and narratively can never be collapsed into one single "real" storyline and so someone like Bashir can never really destroy it let alone join it. I think other shows bringing S31 back as a kind of legitimised known organisation was a mistake but was inevitable. On the other hand I did kinda like that in Sid's audio stories he went with a similar idea and had Bashir as an S31 operative, although even there it isn't really needed as such. I always wanted Julian to just keep being a really good doctor.