no, according to Caretaker after their two week trip he was going right back to jail, and Janeway would give him a good word at his next review
Yeah, that's what she said - but not necessarily what she was planning on really doing with Tom afterwards. She certainly wouldn't promise too much, but promising less than was coming would be a good tactical move in bribing the somewhat likeable criminal.
Tom's conduct in "Caretaker" wasn't particularly saintly, so what made Janeway "change her mind" would be either the unexpected circumstances, or the fact that she and Starfleet had been planning on absolving Tom in the first place, or then both. Certainly the ship still retained a working brig for Tom to inhabit (and this might have been the safest place for him aboard a ship full of Maquis) if Janeway wanted to stay true to her word.