Isn't it odd that Terrorist farmers, terrorist political dissidents and terrorist psychopaths were included into the chain of command but the grand daughter of an Admiral virgin to all the wrong doings in the galaxy was allowed to sit this one out?
The maquis were drafted prison labour who most people back home would have wanted to see buried in a mass grave after all the bollocks they put the federation through leading up to the Dominion War. It was fair game to play fast and loose with their civil liberties considering they didn't even accept that they were federation citizens, and at least some of them who had would up living in cardassian space when the border shifted were actually Cardassian citizens (Maybe that's what Jonas was all about? No? He was Starfleet. Must have been a sex thing.) after being disenfranchised by the Federation...
And on the other hand an Admirals grandaughter.
Any thought about informing the young lady that she was a petty officer in charge of scrubbing manifolds until she proved herself (Lets face it if this was a meritocracy, Seven should have been the Chief Engineer and B'Elanna would have had to have stepped down gracefully just like Carey stepped down Gracefully.) would not have gone down well in the beginning.
That is also certainly why Tom got Pips instead of a rank badge like all the rest of the Maquis, what with his father being an Admiral, Janeway would have been equally careful of the political fallout from roughing up either Seven or Paris.