Seven was refused entry into SF yes, and by the time Janeway threatened SF with her resignation over it, Seven decided not to pursue the idea anymore (this indicates to me that Seven wanted to stop Janeway from going any further or her account.... and she joined the Fenris Rangers by then too).
One of the possible reasons why Seven may have been denied to be part of SF may have been exactly because of her disdain for authority.
Its also possible that Seven's 'interpretation' of SF's decision may not have had much to do with the fact she used to be Borg... or it may have factored into theier decision but wasn't a prevailing detail.
If you recall, when Icheb originally applied to be admitted into SF, he asked Seven to join him, but Seven told him she wasn't particularly interested (its also possible she changed her mind over time once VOY returned to the AQ).
Its possible that given their special circumstances, SF would have been more lenient and allowed Seven to join SF while VOY was still in the DQ because the ship would have needed more experienced officers if it took more time to get back home (like it took an extra 16 years from that point before future Admiral Janwaay changed the timeline) - and its also possible that this is why SF was more lenient on Icheb.
VOY needed more officers, and from SF's point of view, the ship was still about 30 000 Ly's away (it wasn't until the end of Q2 episode that we saw them pushed by Q closer to Earth by about 14 years because of what Janeway did for Junior).
So, in this instance, when the ship returned to Earth in 'Endgame', all of VOY crew service records were examined by SF. Its possible that given Seven's butting heads with Janeway and authority was more of a problem for them, and the fact she just barely started to operate on a more 'human level' (she wasn't butting heads as much in the last year or two) maybe just wasn't enough for them to admit her into SF (but I would be EXTREMELY disappointed that SF would discriminate against Seven just on the grounds of her being ex Borg).
And SF may not have had reservations about the Maqui on VOY... or at least, Hayes mentioned in his transmission to Janeway that he wanted to discuss 'status of the Maqui'... remember that Janeway mainly had an issue with that because she no longer considered the Maqui as Maqui, but SF crew... and also composed a response with Chakotay (which could have changed Hayes' mind about them), and Chakotay was seen as the Captain of the USS Protostar in 'Prodigy' (which is canon - and I was SO happy to see that - we need more of Chakotay in prominent position and to be used properly).
Then again, Chakotay, Torres and Paris all at least went through SF academy. Chaktoay already had a rank of Commander before being reinstated by Janeway, whereas Paris was given a field commission of Lt (he probably already had it before his 'incident' or was close to it - so again, simple re-instatement by Janeway and promotion - whereas Torres would have been the only one to have 'skipped' ranks and given a commission of Lt right off the bat - though to be fair, she didn't advance in rank for 7 years, so its likely that would have been considered her time of 'catching up' if she wanted to advance further when VOY returned).
But I would be of the opinion that the Maqui on VOY weren't seen as a threat anymore by the time the ship returned in Endgame, and to be fair, they ALL served mostly with distinction during their time in the DQ (plus the fact VOY's Doctor told SF originally what happened to the crew, Hayes' response I guess was understandable... Janeway merely 'corrected' the view that she saw the Maqui as separate of SF or UFP anymore in her communication with Hayes).
Most of the differences they had were left behind in the first year of their journey (so SF would have to take that into account)... and the Maqui were still ex Federation citizens... so, its likely the ones on VOY were all pardoned, and given what transpired with the Dominion War, the Maqui would have no recourse for revenge because Cardassia was ultimately beaten in the war (I wouldn't be surprised if some of the ex Maqui from VOY decided to go to Cardassia to try and help them build a better future - now THAT would have been behavioral progress and interesting - but admittedly, probably not for ALL of them).
Heck, even Torres managed to cooperate with a hologram of a female Cardassian engineer... she just had to get to know one which didn't share the military's tendencies.
I would surmise however, that most Maqui from VOY were just free to pursue their own things (if some wanted to join SF, I don't know if they even would have wanted to do that given that they were initially THRUSTED into it, but serving on VOY may have opened for them other opportunities)... and the ones with active field commissions like Chakotay, Torres and Paris (as brief as his Maqui excursion was) were retained in SF (would be nice to learn that both Paris and Torres had a hand in creating the Proto Warp for the Protostar).
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