dark as possible. It's totally possible that he was told the original investigation found no wrongdoing so he continued on in blissful ignorance assuming his friend was no monster. We'll probably never know exactly what JoePa knew or understood. To me, though, it seems so unlikely that he'd risk his own legacy to protect a dirtbag former employee that most of the conspiracy theories make little logical sense.
This was the closest to inside information I ever had on the situation:
http://www.cougarboard.com/board/message.html?id=7742288