Who decides a promotion? Field promo, their commanding officer/superior, sometimes temporary. A captain or superior can recommend a permanent promotion; can they enact it without approval from the higher-ups?
		
		
	 
In this unique situation, Janeway had considerable authority. And she did a lot of things with it.
- Reactivated Paris and Chakotay's Starfleet commissions at their prior ranks of LTJG and LCDR.
- Gave Torres and Ayala commissions at LTJG, and Seska at ENS.
- Took on several Maquis and Neelix as enlisted crew.
- Promoted Torres to Chief Engineer.
- Promoted Tuvok to LCDR.
- Demoted Paris to ENS.
- Stripped five Equinox survivors of rank.
- Promoted Paris back to LTJG.
In light of all that, promoting Ensign Kim to LTJG would not be a big issue. Especially given that Lt. Durst was killed, leaving a vacant lieutenant's slot in Operations. So Harry's line about "command structure" was complete BS.
Yes, upon Voyager's return, or re-establishing regular contact, Starfleet could have taken over and ordered Janeway to undo any of these actions, or promoted certain crew themselves. But they would have had no issue with giving an outstanding officer a scheduled promotion. Indeed, it's odd that they didn't instruct the captain to do so.
SO...
FOR: Harry was an excellent officer and deserved to have that fact acknowledged. 
AGAINST: There's no "against" argument that has survived my counter-arguments.