It definitely is a football issue. They decided to cover it up because they thought it would harm the football program. Once they decided to cover it up, the cover-up allowed Paterno to keep coaching football. That's how it resulted in wins. No coach Paterno, no wins, at least for coach Paterno. So you vacate the wins. Think of vacating the wins as retroactively firing the coach. Instead of Paterno getting fired in 2011 for the cover-up, he would have been fired for the cover-up in 1998 had everyone known about it, and he would never had the chance to have won those games.
But this isn't just a football issue. Paterno was a leader on campus. We hold leaders to high standards. It's not good enough to walk a line between legal and illegal. Kids got raped. He is culpable because he allowed a rapist to remain on campus. Had he turned Sandusky in, kids wouldn't have been raped. If he hasn't committed an illegal act, he certainly committed an immoral one, one that is unacceptable for a leader of his stature. That is a fireable offense.