What Janeway has no problem with is promoting the Maquis, from zero to hero, at will.
The only person whose "promotion" I regard as questionable was B'Elanna.
Chakotay was a 20 year Starfleet veteran and a lieutenant commander, before resigning from Starfleet. Tom Paris had earned LTJG before getting expelled. Janeway simply restored both men to their pre-termination rank. Given the extreme circumstances, both those decisions made sense.
Ayala was field commissioned as a lieutenant. But he was one of Chakotay's most trusted people, and he was subordinate to Tuvok, just as Chakotay was subordinate to Janeway. Most other Maquis were commissioned at ensign or crewman.
As an academy dropout, B'Elanna probably should have been commissioned as an ensign at the highest, and been subordinate to the highest ranked Starfleet survivor. Janeway's decision to make her chief engineer was ostensibly because of her skill, but really because the writers wanted a certain character distribution: three Starfleet, two Maquis, one in-between (Tom), one computer program, and two local civilians.
A more sensible pattern of character development for B'Elanna would be for her to get brigged for punching Carey, then be allowed to serve as assistant engineer on her release. In "The 37's", Carey and a few others jump ship, and a calmer, more cooperative B'Elanna is ready to assume the top spot. But as we already know, Voyager's writers wouldn't have known "sensible" if it ran over them with a bulldozer.