Title IX, BYU Police, and Provo Police should have no communication with the honor code office. The girls should be able to report their rapists without fear of the HCO.
However, I think if the HCO is investigating someone who was a rape victim, and they found out through a different source that does not include the accused rapist or his friends, then there could be consequences.
My biggest problem with the whole thing is people in positions of trust for rape victims reporting to the HCO on the crime.