IF Starfleet still held it against its former officers for having dishonored (and betrayed) the organization in particular, by using the miltary training received to pursue criminal activities or activism, B'Elena Torres & Tom Paris would be those who would do best (1), because of their personal ties with a Starfleet Admiral (even if Owen Paris hasn't done a lot to protect his son after the Caldik Prime's accident - in the same time, what Tom's behavior was too serious! -, he will everything to catch up and behave more as a beloved father and about B'Elena, even if he doesn't appreciate her more than or still holds it against him for her past in the Maquis, she is is nonetheless his son's wife & the mother of his granddaughter, so, he will do his best to protect her too) & Captain (Janeway has always had a protective feeling for him & let's be honest, Tom had to prove himself worthy of her trust and a talented/sensible officer. And the same for B'Elena).
(1 ) The one who would be the more at risk (= with a stiffer penalty of imprisonment as seeing as death penalty isn't a conceivable punishment anymore), would be Chakotay, not only as a former & highly experienced senior officer but as the leader of the Maquis crew (usually, it is easier to take the fall guys but in military cases, it is often the leaders or ordering parties, who are searched and the most severely punished).
And I want to clarify, before being accused of Chakotay bashing, that I say that because of my personal experience of military discipline (2) and it is precisely that said experience, which makes me say that there is little chance and even none to see Starfleet and its bunch of admirals (except Janeway, who has come to know them) agree to recruit the non-Starfleet trained people from the Maquis and/or to rehabilitate and restore the former officers in their ranks after Voyager and from my point of view, it is natural. Indeed, it is not only, for Starfleet, a question of reputation but, it is too, the best to do to protect its rear (if these people - Maquis crew - were able to switch in the criminal activism, betraying by the same, the Federation and/or Starfleet policies for some of them, once, what would prevent them to do it again, by this time, diverting skilled crews, powerful vessesls & weaponry that they have been assigned with confidence for commissioned assignments, the next time a new peace agreement with a hostile alien population would be signed (with a risk of desire for hegemony from their part)?! Anyway, both organizations would NEVER take the risk of being betrayed again and/or endanger their people.
However, to be able to keep all these talented & trained people under its fold (and eventually monitor them to avoid unpleasant surprises, whether they have Janeway's and/or Owen's support), Starfleet with the consent of the Federation of course, could recruits them as civil personal and/or unofficial armed workforce in some politically sensitive issues
(2) Since I actively participate in this forum, I never said anything on me, like most of you, by the fact, right?! Well, I'm a jurist in criminal law in civil BUUUT, I started my professional career ... as a sort of ADA in the departement of military courts -> the french equivalent of the US JAG, if you prefer). And regardless of the country and/or the era, let me say that Army is always harder on those who have turned against military institution and its values/policy.
I regret that as well the producers as script writers for the TV show AND authors of post-Voyager novels, were so disinterested in the military topic, which is a so strictly codified & disciplined universe, especially these latter, because if they had informed more, they would have NEVER allow the former Maquis to officially become Starfleet and still less, made Chakotay, a Captain!
