It's not about guilt, it's about trust. They were trained for years in an institution that violates trust as a matter of course. That makes them suspect and the judgement completely fair.
Lots of universities have had scandals. I could probably dig one up from your alma mater. They're big places with long histories. Collective punishment achieves little productive and should be avoided.
Collective punishment is a clear and unilateral signal that something is extremely wrong and not within the punisher's power to unwind properly (or prevent in the future). Until it's clear that this university can be trusted, they should not be. I would feel the same about any schools that I attended, and I would not have issues with blanket bans for them either if this was the kind of activity they got up to.
Their graduates might not have been directly involved, but it's not possible to ig ore that those graduates were the product of an academic environment where this kind of behavior was not only sanctioned from the top but also defended as an adequate use of resources.
Adequate use of resources seems like a bizarre reasoning. Do you also evaluate how a candidates alma mater compensates its football staff before you hire?