I haven't tried it, but since the eyes don't have any edges in common with the rest of the mesh, you could probably cut them out of the mesh (or duplicate them, and make the originals invisible). If you leave them in the same place, with the same hot points and parented to the head, it might work. You'd lose any morphs for the eyes, I expect, but you should still be able to rotate them where you need them to be, then you can do anything else you want with them since they'll be free of the figure's skeleton.

I did a horror pic once (in another app) where I did something like that, a skeletal figure putting on human skin and eyes to pass as human, and the disconnected eye part worked fine.