A field commission is a perfectly legitimate commission. And there's no reason to bust the guy back to commander after he's saved the Earth.
Now, I understand there's no ship for him to take command of...and it's just awkward to have Picard call him "Captain" for a year. (Though that can just be avoided by always referring to him as Number One.) But let's say you're Rick Berman, and you don't give a flip if your show has serialized elements...how do you fix this?
Myself, I offer Frakes DS9*, and go with either Shelby coming back in a year if the actress wants to, or with Data as XO.
*It could work! Don't be hatin...