I think if Mulgrew was written out they probably would have found some other Starfleet captain who got stranded in the DQ to take over for the last season.
Although I think making Chakotay Captain, if it could revitalize Beltran's enthusiasm for the role with more scripts and some new situations, it could have brought back the Maquis conflict. Chakotay making decisions the Starfleet officers disagree with, Starfleet officers questioning his right to be Captain because 'He was only made first officer to appease the Maquis', Tuvok defending him even when he disagrees with the orders.
I guess I have a higher opinion of Beltran's capabilities than some others. I think he worked well in episodes like Equinox and Course: Oblivion. And I think in those kinds of scripts that side of him would have come out.