The show, shows them like that, with Bashir literally getting recruited after playing James Bond in the holodeck many times and that’s actually one of the arguments that Sloan uses to justify why he should join. Malcolm Reed, who “surprisingly” is also a british character feeling like he’s the coolest guy ever, who is too cool to even answer when someone asks if he likes the food, turns out to be from section 31 too. And in discovery, a certain emperor joining section 31 after showing a lot of “cool moves” and high-tech gadgets that are probably possible to find in some James Bond movie.
As for starfleet, if it is a military organisation under a democratic regime, then it has to follow the same laws and regulations. I am not aware of any military group that can blatantly ignore the law and face no repercussions, in any (pseudo) democratic government. And Discovery doesn’t portray it as illegal at all, explaining that it is at the center of almost all of starfleet’s decision (if I remember properly, an admiral explains that all decisions are first processed by a computer owned by S31, to get an automated suggestion of the decision to take). Such a central element cannot be simply hidden, it has to be allowed by the federation.
As for science fiction, I do not agree. Science fiction is about taking another time/place/context to put the focus on current problems, whether by exaggerating/worsening them, removing them, or isolating them. If you show earth in 300 years and nothing changed, it’s not science fiction, it’s just a fiction that does nothing except change a date. By not showing any difference in how illegal groups like that are handled, the show doesn’t say that it is bad, but instead implies that it is something that never changes. And it is said directly, that S31 existed for a very long time and that it is still here, which implies that it will never leave. Which in turn, encourages apathy on the subject, telling the viewers that it is useless to fight against such groups, they’re just a “constant of the universe”. It is probably not the intended message, but it is the result.