Near the end of episode (Parallax) Chakotay asks if things went differently and they were on a Maquis ship now, would Janeway serve under him. She deflects it.
Incorporating any changes you feel like, (Bigger Maquis ship or whatever) what you think would have been like?
I imagine if Voyager was destroyed in an idealistic decision to help the Ocampa, that the Maquis ship and crew, less advanced, would have resorted to piracy. It would have been Seska's time to shine. They'd probably hijack several vessels.
I don't think Janeway would have mutinied, but I definitely see her peeling off with a substantial amount of crew within a season. Chakotay seems the type that would set the ship on park at the 37 planet.
If you really want to flip the script, have Chakotay be the Starfleet Captain and Janeway as the Maquis rebel. It would have fit her, I think. Especially season 3-4+ Janeway.