I think that McQueary is the convenient fall-guy for everyone.
He was a graduate assistant in one of the most powerful football programs in history, under one of the most legendary coaches of all time and the person that he would be accusing was also a legend who was the founder of a charity for children that was not only raking in millions of dollars, but had affiliations with some of the most powerful people in the state. Look at his options:
1.) Beat up Sandusky and rescue the child. If he had undertook this action, he would have immediately been arrested regardless of the situation and Sandusky and his powerful allies would have had time to cover up everything. The child would have been threatened, most likely, into not testifying against Sandusky and the attack would have been attributed to some internal feud within the athletic department. McQueary would have been surely convicted of assault, lost his graduate assistant position and then likely never been offered another opportunity anywhere.
2.) Go to the police. He allegedly did this and there's now no record of it. If Sandusky's judge has connections to his charity, it's likely that many police and other municipal officials did also. His complaint was probably lodged and then the athletic department and administration at PSU offered their "assistance" in the investigation. Sandusky denied everything, his reputation overwhelmed the credibility of McQueary and then an unofficial arbitration probably took place between Sandusky's power structure and a completely powerless McQueary: forget it and we will too. Fight it and become part of the Poconos.
3.) Go to JoePa and attempt to gain an ally that has the power to actually do something that won't necessarily turn you into a John Doe in the morgue. If JoePa (the most powerful person in the area) says that he'll handle it, then you can claim that you went to the ultimate authority and the culpability falls to him. If nothing is resolved, you will have to fight your conscience and you will lose respect for that authority in which you put your trust, but you had to protect yourself within this environment as well.
4.) Go public. McQueary could have gone public after his other actions failed and it might have worked to bring down Sandusky. However, a single accuser against a legend with a lot of powerful allies must have some proof or some allies of his own. The children that were being victimized were being helped by this charity and there's no telling what types of threats and other leverage would be used to keep them in denial. I doubt that many of the power structure at PSU would have supported him because what is happening now would have happened then. Once again, he likely would have been discredited, destroyed and maybe even worse.
I think that far too many people either think completely with their heart, they let outrage skew their visions of reality or maybe they're just too naive to understand the amount of inertia that McQueary would have been forced to overcome to really effect any scrutiny upon Sandusky at that point, given their diametric positions and reputations within the program at PSU.