Look, there is no easy answer to dealing with alleged rape cases. The overwhelming majority of rapes are committed by someone the victim knows. So inevitably, unless the rape was video taped or done in front of witnesses, it is going to be a case of he said, she said. Because of that most rape cases don't even go to court, let alone end in conviction.
I certainly don't want to abandon our "guilty beyond all reasonable doubt" standard but one of the consequences of that is most rapists will remain free. And yes, sometimes a woman will falsely accuse a man of rape. But the crime of false accusation also cannot easily be proven beyond all reasonable doubt because, once again, it is usually a he said she said case.
In the end, you will usually end up with a rape victim who feels she never received justice and is forced to keep attending the same school as her rapist unless she drops out or you end up with man who was falsely accused and his life is likely ruined to some degree.
Both scenarios suck. There isn't an easy solution to it. But I really am not comfortable with universities being the ones to handle these investigations.