I don't know how one can dispute Joe's seminal influence on Penn State. He didn't do it by himself, he built on the work and institutional values set by those before him, but, through Joe's personal vision and willfulness, he pushed Penn State forward to a degree that is matched only be a handful of luminaries in the entire history of American higher education. And no one who is/was a coach had a similar effect at improving public perception of the school he coached, and I include Bryant, Rockne and Wooden in that assessment.
But nothing in the above paragraph implies that Joe was somehow a human being without flaws and vulnerabilities or one who never made mistakes. I believe Joe stayed too long and grew too powerful, for reasons that are easily understood and maybe couldn't have been prevented. And the above paragraph doesn't say anything specific about Joe's role, good, bad or indifferent, in the Sandusky Scandal.
Joe's legacy remains a work in progress, because all the facts are not in. I do think Joe, in hindsight, had some regrets about how he handled McQueary's report, and those regrets, however immaterial they may turn out to be in the final assignment of culpability, are part of his legacy, too.
I can't understand why it's necessary to proclaim Joe a saint or denounce him as a sinner. He was a lot more complex than either description. But appreciating such complexity takes some brain sweat, and most of us are intellectually lazy.