I am just saying either is likely, not least as any surviving Maquis would have by default ended up on the Starfleet side during the Dominion War.
Ended up by default on the Starfleet side doesn't guarantee you a job among their staff and/or crew, especially after to have been considered as terrorists and/or traitors.
-> Besides, IF Starfleet was really ready to give a chance to their former officers, admirals would have informed Janeway of their intention (at least in s7) to formalize the current commissions for those who wanted to stay within the military instition, promising a place on their return from DQ. Instead of that, the blur persisted until the end as if the producers/writers wanted to let fans choose the end, at least one that suits them best (for me, it would be no amnesty or pardon but a suspended sentence for services provided on board of Voyager and of course, no chance to return to Starfleet for former officers or even new apllicants. They cannot have the cake and eat it too, the chance should not be carried too far.
-> to hold beliefs and fight for them, is a good and important thing but to be ready to assume the consequences of their actions, including former ones, is essential too). Believe me, this situation would be a clear picture of the real conditions!
By the way, it seems to me that, in Renegades, Cordero/Chakotay is no longer in Starfleet but owns(/works in) a bar... .
However to pick up on one point you make...I was deliberately ambitious by not mentioning Janeway by name.
Whatever Janeway or Seven (or even, Seska), Chakotay has the bad habit to ALWAYS set his sights on women having strong personalities. Result: they ended quickly tire of him or were not interested at all.

Again, neither Janeway or Seven needs Chakotay to achieve their aims. However, he needs Janeway's protection more than Seven.
One thing I am not fond of in the relaunches is the destruction of relationships the show ended on...Bashir and Ezri splitting up was a bad idea, and tbh, I think more should have been done with the Seven Chakotay relationship...I know some fans didn’t like it, but it made a fair amount of sense, and it is what we had, as well as being an important motivator for futur Admiral Janeway. I can see the flip side, and the fan edit of endgame that turns up where they extend it with bits from other episodes and make the relationship into Harry and Seven is quite nice mind you.
I do also see the Chakotay Janeway relationship early in Voyager but...like I said. It ended with Seven and Chakotay.
I agree with you on this point, Star Trek and romantic relationships never managed to go along. Who knows why?! Even Paris/Torres, the only couple which managed to last through the seasons (and even started a family), was odd for me. In fact, I never found them a good match to one another... , contrary to Janeway/Paris and that despite the age difference* & subordination link but if Janeway always refused to date Chakotay because he was her XO, I don't see her suddenly agreeing to date her younger pilot, as bright he is, rightt?!)
-> as for the age difference, if some people found C/7's romance acceptable
despite their almost thirty-year gap, they shouldn't be shocked with Janeway/Paris! (I'd add that Roxann Dawson is younger than Kate Mulgrew of only 3 years!)
About Chakotay/Seven, sorry but I am one of those people who didn't like this pairing (I did not like J/C either, btw). Not only their story was badly tied (seriously, these 2 people had to share something like 3 or 4 scenes together since the arrival of Seven on board, in s4 and their relationship was tinted of disdain for the most part and suddenly, they dated, in the last episode of the series?! Sorry but producers/writers really took the most of us for fools to think that we were going to believe this humbug. Without forgetting that both actors really made little effort to be convincing! -> for me, the characterization of Chakotay & Seven lost a lot in this relationship (warmth, emotion, innocence, mystery and authenticity) and all this to give Robert Beltran a bone to gnaw! What a waste of time! :-(
-> It seems that their separation soon after return to Earth was acted like an irremediable event by most authors. of non-canon novels & fanfictions for making J/C or J/7, some possible pairings.
-> maybe I missed something but it seemed to me that Cordero/Chakotay was single in Renegades, right?
In terms of living her life...her wishes wouldn’t have been a factor, it would be about what Chakotay chose, and in the books there’s a fair amount of his reasoning behind his choices, including the Borg invasion.
Could he go a different way?
It seems to me that Chakotay never accepted Seven's borgess side. In fact,
he really started to be interested in her from the moment she seemed more human, in the approach of her humanity, while mainly Janeway and the Doctor (yet a hologram who tried to be/act like a human), always accepted/understood Seven's both sides. It is still quite surprising from him (his hostile attitude towards Borg, despite all meetings he made), while he seems so open.
Sure. But he was Starfleet longer than he was Maquis, and he couldn’t even start a fire. I don’t see him farming, but can imagine him trying for good reasons. I guess good reasons is what Chakotay always uses as motivation...so we are full circle...both are likely outcomes for the same character.
The fact that Chakotay was unable to start a fire was especially the fact of his performer, Robert Beltran, who has never learnt to start one. It is just unfortunate from his part, to have made so little effort to better prepare his role by himself. I remind that Chakotay was supposed to be familiar with Mother Nature, what means, to be able to able to start a fire, to find food and be able to hunt animals if necessary, to build a hut and/or a small boat -> Resolutions showed that he was able to build a wooden bath, right?!). In short, this does't mean much.
By cons, what surprises me the most is that, despite the resignation of his Starfleet commission to join the Maquis (and the violent actions he later led in its name, sometimes against his former pairs), he still wishes and be allowed to return in the military institution, recover his former commission (and why not a promotion) and get a place of a teacher at the academy. Seriously?!

This guy acted as a terrorist against the Federation and fought Starfleet during his time in the Maquis and he wishes to come back as if nothing had happened, under the pretext of having contributed actively with Janeway in DQ... . Bah, hope springs eternal fools!