The legal system absolutely determines if a crime happened. However, Rutgers (just like any other business) has the right (and probably the duty) to determine if an action by any of its employees or students (who are in a quasi-associate role) can or will bring negative publicity to the school. And if it does determine that, it has the right to take a corrective action if it chooses (as long as it is permitted by law or contract).
In this instance, if the school determines it's more likely than not that a crime occurred and it chooses to suspend a player to demonstrate to the world (and its other employees and students) that the school does not tolerate that behavior, there's nothing wrong with that.
The problem is when schools (and other businesses) use zero tolerance principles ("There is an allegation, so we're not even going to investigate, we are just going to penalize and sort it all out later,") or when they use inconsistent penalties for similar behavior, or when they fire someone they don't believe did anything wrong simply because they want to escape bad publicity (ie, Mike Rice).