I think he should be allowed to compete, but on an "exhibition" basis. Since the question of advantage/disadvantage can't possibly be answered, I don't think he should be eligible for any of the regular medals in his event. But if he's fast enough to make it to medalist level, give him an additional medal. If he comes in third, give him a bronze medal, but give the normal runner who finishes fourth one as well.

Apples shouldn't be allowed to compete against oranges, but that doesn't mean they can't both be in the same salad.