You know what would have been a daring and fantastic Choice?
Having Neelix and/or Kes JOIN THE MAQUIS!
All they had to do for Marquis initiation is get drunk, kill a Cardassian and have sex with the Maquis leader which is probably still Chakotay and not Janeway who hadn't seemed to have eaten his responsibilities, duties ad benefits as the Political head of the Terrorists on Voyager... Although considering there are almost no Cardassian's to gut and pitch on a pike in the Delta Quadrant, and Chakotay is undersexed, the amended initiation rites probably wouldn't be so challenging.
Janeway couldn't let them join Starfleet, and they don't want to be antisocial or excluded, so why not join the Maquis if it doesn't really "mean" anything?