I'm not a lawyer, but I believe the presumption of innocence is relevant only in the justice system and not extended to privileges offered by the institution. It is a privilege and not a right to rent dormitory housing as well as a privilege to be an scholarshiped athlete at the university, so the university is within its rights to suspend those privileges. I would hope that they wouldn't do so unless it had strong evidence to suggest there was wrong doing by the student-athletes. There must be significant evidence that the staff member, whoever that is, participated in concealing information from other university staff.
Unfortunately, there is no way of swiftly and reliably judging the case fully before the legal process can take place. But, what if this student-athlete were not removed from the dormitory and committed a second sexual assault at the dorm? The university is at significant risk and has to take actions based on the weight of evidence that a violation may have occurred to protect other students.
It's possible that this S-A could win his case against the charges or even be exonerated, yet still have to suffer disruption to his life and reputation while appropriately receiving "due process". The biggest issue is whether the "due process" is fair, impartial, and not political, which was proven not to be the case with some of the Gopher football players.
Let's hope this situation is fairly judged, but I can't blame the football program or university for taking the actions that they have unless something is revealed to show that they made the decisions on weak information.