Actually, the model doesn't need anything more than a simple rotation in PCS2. No need to remake it or anything like that.
I've been thinking about doing exactly that. However, it's been that way since Retail, and many campaigns have opted to just rotating the model's position in FRED and calling it a day. (Like: Derelict). Which would mean that not only would a corrected model have to be included for them, but their missions would have to be corrected as well. Or the older, non-rotated model provided for use.
This issue is currently under deliberation. There is a fixed-point orientation model (it even has docking points and path's applied to it) around here some where. But at the moment, that version is not in the MediaVPs but I'm hoping it will be for the next Release, specifically because of this problem.
(Unfortunately, the problem then get's even MORE complex when you go to play a "Made for Retail" scenario and there is no older, non-rotated model in place, instant breakage)