I am going to take issue with Geoff on this: Penn State University as an institution was being punished. And if Penn State cannot be punished, then the entire scheme of NCAA regulations is unenforceable (and humor me for the moment and assume NCAA regs are worth enforcing). Any long-lasting institution survives its individual members; old members are replaced by new members, but the institution is understood to survive uninterrupted. And the institution bears responsibility for the conduct of its members--past, present, and future. The players and coaches who break rules are always gone by the time enforcement comes down. If that punishment is wrongful because current (rather than rule-breaking) players are in the institution at the time of enforcement, then punishment of the institution always becomes wrongful. Even in a case of lack of institutional control (as Penn State arguably was), the institution could always argue that its failure was to control previous players, but that shouldn't be taken out on current players. But then the university gets off scott-free and has no incentive to police its future members, because it always can argue against punishment falling on its current players.
Taken to its conclusion, Geoff's argument applies to any institution and institutional punishments. Germany should not be made to provide reparations or other compensation to Holocaust victims because the punishment falls on the current German government and citizens; ditto for arguments with respect to slavery. International law (which I rarely cite or discuss) recognizes the concept of successor governments. Why not for universities in the field of NCAA enforcement?
All that said, I agree with Geoff that this is an example of "punisher's remorse", a term I wish I had used in a radio interview I did last week. But the remorse is over punishing Penn State--the NCAA does not want one of its flagship institutions under such a harsh punishment.