I thinking catching rapists is the strongest policy issue involved, because (I hope) it means there will be fewer rape victims.
However, I really dislike the fact that the reason the women are not reporting the rape is because they will face a consequence of their own actions that is unrelated to the rape. (E.g., I will get kicked out of school because I take illegal drugs.) The rape victim is faced with this question: Do I want to hide my own sins enough that I am willing to let the person who raped me stay out on the loose?
I sympathize with the position of the rape victim and acknowledge that I, too would want to bury my own misdeeds. The social, economic, & overall life consequences and repercussions are so severe (possibly getting kicked out of school) that I totally understand their behavior.
I also dislike providing an incentive for making a false rape allegation. To be a rape victim is a terrible terrible thing, but it is also devastating to be falsely accused of rape.
Mix these all together and you have a big quandary. I think my preferred approach would be to make a clear statement in the Honor Code that no student will be kicked out of school for their first "major" HC violation, unless the student refuses to agree to change his or her ways. Then the University can say students should have no fear of going to HCO, because there is a built-in mercy rule.