Each time I watch this episode, I carefully try to follow the cubes through the scene. I agree that the director/crew got it right - the female crew member's cube was destroyed.
I can't say what Rojan was thinking when deciding which to destroy, but the writer certainly did give it thought. In destroying the woman's cube, it gave a greater impact to the story - remember the context of the time.
As an aside, when watching the episode I often wonder did the restored crew member have a headache, or other assorted bumps and bruises from being tossed about while in a 'dehydrated' state?