Again, I'm deeply convinced that EVEN IF Chakotay was pardonned*, Starfleet would never reintegrate Chakotay into its ranks again and still less, entrust him the reins of a vessel. The reason? Regardless his invaluable experience, first as a Starfleet senior officer then as a Maquis leader, this guy is simply unmanageable, especially when he takes seriously the cause of a person or a small group. Plus, no matter my unliking of him, I must admit that as Janeway, even if people wouldn't appear necessarely to be too much intimidated by him, yet radiated an obvious though unspoken respect for him, which could lead some "weak" officers to follow him easily.
In short, all that (his experience, his personality, his natural leadership) would still represent a huge potential danger for Starfleet and incidentally, the Federation. And neither of both organization has interest to put the fox (or the wolf as seeing as it is his spirit animal) in charge of the henhouse, right?!
That being said, as I have said once, nothing prevents Starfleet to use Chakotay's invaluable experience in specific (and why not secret) missions, in exchange for a certain freedom of action and legal protection while keeping an eye on him, as Starfleet is not engaged officially.... .
* Usually, the penalty is reduced, thanks to the huge support of a commanding officer, but never completely extinguished, situation which forces the culprit to stay on the straight and narrow.
-> what is valid in civil life, also in the army but with more discipline & organisation.