punish a program, or a school. You can only punish people, and the people who would be punished did nothing wrong. But, as you pointed out, calling for it makes people feel like they are morally superior somehow.
Those calling for the death penalty for Penn State remind me of those who tell me that I owe some kind of debt because over a hundred years ago people with the same color of skin as me owned slaves. In both cases something terrible happened, and some people pretend like punishing people who had nothing to do with it somehow makes sense.