If what you say is true, then why did Joe not confront them, even if it meant he would no longer have his job? If Joe truly was the kind of man as you suggest, it would seem logical he would put up with dealing with them.
that should be “it would seem logical he wouldn’t put up with dealing with them”.
I’m just going on intuition here, but Paterno wouldn’t have any reason to have any day-to-day dealings with any of those people. The Board of Trustees ultimately controlled his fate (as you saw) and they have been looking to get rid of him for years. This simply provided a convenient excuse to do so.