I don't think Joe was a pedo. I think he had a narcissistic personality that probably crossed over into a messiah complex as he aged. He truly believed that he was this saintly figure sent to save college football from the Switzers and Sherrills of the world and that nothing was more important than that, certainly not some loser, troubled kids. Throw in the fact that he only and finally won a couple of NCs on the backs of Jerry's defense, and I believe he made a conscious decision to silence the kids and cover for jerry in the service of what his sick mind saw as the greater good: the whole grand experiment, success with honor myth.
In a sense, this is almost less forgivable....that he was a cold-blooded sociopath in covering for Jerry rather than a sick in the head pedo driven by whatever demons they're driven by.