Even if Starfleet is "the principal means for conducting deep-space exploration, research, defense, peacekeeping, and diplomacy", the organization works on the military model (uniforms, ranks, academy), right?! Well, by experience (I'm a former officer who worked in the french equivalence of JAG), I can tell you that usually, military populations, have a very good memory. Result: battles won and lost, exploits of all kinds and crimes survive over the centuries and continents.
(For my part, I noticed that from comminding officers, officers, soldiers and even civilians working for military, use to hold and talk about only battles won with the name of their leaders and betrayals of any kind and the name of their perpetrators! <grin>)
Yes, the world moves but not the military. Indeed, despite technological advances, weapons or even political changes, these people are like frozen in a world where traditions, battles, present feats (exploits of all kinds), honors, infamy acts form a whole and they transmit this whole from generation to generation.
-> cf to Dreyfuss Affair which ran 12 years (even if the officer ended rehabilited, his life was definitively crushed). I could tell you the stories of officers at any rank, who were sent to prisons in the aftermath of the 2 world wars for treason during the conflicts (the most part were shot after a quick trial), and some of them were only pardoned last year, because the charge was not formally supported. And this was possible because the families kept the pressure on the authorities! Oh and lately, I heard that a US soldier who had abandoned his post 20 years ago, just being caught and he was doing jail.
-> in ST: Voyager, I remember how Tom Paris was welcome when he first put his foot aboard Voyager. Most officers had never met him before but all knew what he has done to some Starfleet officers and despised him for this.
Even if the former Maquis crew had to enjoy a certain indulgence, due to their collaboration on Voyager (even if they had in fact, little choice -> die in Kazon's hands or in hands of whatever other species OR live in a relative security with Janeway and her crew), indulgence isn't a pardon and still less, a carreer within Starfleet as some - like Chakotay - would like so much. Some friends of mine, fans of Star Trek, who still work as officiers in disciplinary field, told me that they thought that a pardon was completely reject, and a more lenient penalty with a forced exile was more likely, excepted for B'Elena Torres, who could take advantage.
I'm sure that during the time Voyager was still in DQ, at Starfleet HQ, some Admirals, like Hayes, strove to decide what they would do of Chakotay and his former crew, once they would be back on Earth (= in which prisons will they send them after their trials, etc...) even maybe hoping that some of them would die in space.
On the contrary, I think that because they are humans and that their cases will have a strong chance to be treated with Starfleet human officers, they will be more likely to benefit a certain form of indulgence. Other species could have treated them hardest, especially if they think that strong values, dear to their species, were violated.
