Your scenario and the scenario where someone is falsely accused are indistinguishable prior to a court proceeding. In the second case the victim is the person being falsely accused. Then you would have the same problem with the victim being unable to maintain their academic performance if you kick them out of school without due process.
Let's even admit that forcing a rape victim to live in the same dorm as their rapist is untenable. So that option is off the table and one of them should leave, but in that case it would be the same burden (of leaving) on each class of victim and the tiebreaker should be innocent until proven guilty. On top of that, it may be possible to live in a different dorm or take different classes while remaining at the same school, which is a lesser burden than an innocent victim being forced out of the entire school.
Let's even admit that forcing a rape victim to live in the same dorm as their rapist is untenable. So that option is off the table and one of them should leave, but in that case it would be the same burden (of leaving) on each class of victim and the tiebreaker should be innocent until proven guilty. On top of that, it may be possible to live in a different dorm or take different classes while remaining at the same school, which is a lesser burden than an innocent victim being forced out of the entire school.