Maybe I wasn't writing it clearly enough.
In all of the scandals referenced (Minnesota, PSU, UNC, SMU, current basketball scandal) there is always some sort of institutional cover-up, whether it's by the head coach or the AD or someone. That cover-up is done in a misguided attempt to protect the school or that particular athletic program. The school and the people covering it up should be punished by the NCAA for that.
My point was that with respect to additional punishment for the underlying offense, part of the analysis has to be whether the underlying offense was used to try to gain an advantage, or was it just something completely unrelated to the program. In the Minnesota and UNC cases the underlying offense was used to keep basketball players eligible to help the program. At SMU and in the current college basketball scandal, the underlying offense is the payment of money to attract star athletes to your program.
In all of those, the underlying offense was committed by coaches or boosters or some combo of the two to benefit the program.
At PSU, the underlying offense was the rape of children. Obviously that has to be punished severely by society through our criminal justice system, but I'm not sure that it calls for the dissolving or eradication of the football program as suggested by others. If Minnesota football players raped a girl, they need to be prosecuted, and they need to be kicked out of school. But I don't think the program itself should be suspended for that underlying offense.