Normally, Janeway would normally just send her crew evals to Starfleet. They would monitor officer quality and duration of service, then direct her to promote certain people. If a person's higher rank rated a new assignment, they would transfer them.
With Tuvok, Janeway evaluated his length and quality of service, then granted him field promotion based on it. With Tom, same thing. The Maquis received field commissions: Janeway either reactivated existing commissions (Tom, Chakotay) or assigned them ranks based on their status in the organization (Ayala, Seska) or skillset (Torres).
Compare these actions:
Promotion of a lieutenant to LCDR: Reasonable, but not automatic.
Promotion of a demoted ensign (Tom) back to LTJG after one year: At least allowable.
Commissioning the Maquis: Questionable under normal circumstances. But probably Ok in an extreme situation.
Promoting a brand new ensign who has served competently to LTJG after 2-3 years: essentially automatic. If an officer is stuck at ensign for 7 years, he'll be lucky to get a posting on a garbage show afterward.