How can someone be stopped who is
using this ability to get out of
punishment for crime.
For example, if a rapist got off
because he identifies as a
woman and the victim claims
to have been raped by a man.

This is not serious and a defense like that would never fly in a court of law. It's ridiculous really. If the rapist is identified, his own feelings about his own gender are irrelevant and would be irrelevant under even the most radially left legislation that might be suggested.