Promotions come more slowly at higher ranks. For the USN, five years at lieutenant and six at lieutenant commander is the norm. Ensigns are usually promoted after two, and sometimes earlier.
And in any case, Tom Paris was an ensign. He provided one and a half years of quality service, and was restored to lieutenant. Why shouldn't Harry be granted that same rank for six years of being "one of our best people"?
And they would have. If Janeway had paused a senior staff meeting, called Harry up to the front, stuck a pip on his uniform, and declared him promoted to lieutenant... I cannot imagine Tom or B'Elanna doing anything but congratulating him.
Janeway can make field promotions on her own say so, but there is a process for the promotion to be "real".
1. Quarterly Evaluation by the Councillor and XO,
1a. Reviewing recommendations from the section heads for promotions, demotions, and transfers.
2a. Interviewing staff recommend for promotion, demotion, and transfers.
3a. Write up Quarterly evaluation, present to Captain.
2. Captain reads, maybe amends the Quarterly Evaluation, rubber stamps it, and sends it off to Star Fleet Command.
3. Starfleet Command reads, considers, and proffers new orders for promotions, demotions and transfers, then sends them back to the ship.
4. Captain reads the new orders, and then acts like it's her idea to promote, demote and transfer every one that is promoted, demoted and transferred.
So?
All promotions and demotions and transfers on Voyager, in the Delta Quadrant, cut off from Starfleet Command, were field promotions or illegal promotions, demotions or transfers. All field promotions have to be ratified by Star Fleet Command "eventually" to be made legal.