Exactly how many years of winning coaching is the minimum to excuse covering up for a child rapist? Art Briles has done really good things in four years at Baylor, but I assume that's not long enough. But did, say, Bobby Bowden put in enough years that it would have been OK for him to willingly cover up some forced sodomy?
Anything good Paterno did in his coaching career -- be it on the field, seeing players graduate, donating money to the university -- are all completely overshadowed by his allowing a predator to go on raping kids, even letting him onto PSU athletic facilities to do it. That's Paterno's legacy. That's all of it.
I actually have far more sympathy for McQuery than for Paterno, because I can understand the mechanism behind his failure to stop what he walked in on. In psychology there are a couple of principles called cognitive dissonance and denial that would come into play. Basically, when suddenly confronted by something completely shocking, completely unexpected and completely out of the norm of what is typically expected in a certain circumstance, then the mind often simply refuses to believe -- temporarily, at least -- what has just been witnessed. If what was witnessed was seen only briefly, then the subconscious will try to rationalize what was just discovered, trying to turn the out-of-the-ordinary event into something ordinary. A really common example of this is people refusing at first to accept the sudden death of a loved one. It's almost a sure thing that McQuery didn't fully begin to believe he saw what he saw until some time later.
Still, McQuery's coaching days are more than likely done.