You can't have an ensign as captain
Ah, but remember that as soon as Harry gets out from under Janeway's boot, he ranks up quite quickly.
My scenario... after Janeway makes admiral, either Chakotay or Tuvok take over as Voyager's captain, and they make Harry their first officer. Voyager happens to be in the sector when Freeman is taken, so he is assigned to command the Cerritos for the duration.
Before he departs (upon Freeman's exoneration), he and Boimler share a moment, and he reminds him that he knows what it's like to have to wait for a promotion.