Well, I think the writer (a very good one, who I’ll now follow) is speaking from an administrative standpoint when he talks of js being an ex-assistant.
I think the important points are that up and until Joe’s testimony and eventual firing, all we had was victim #2 (McQueary/shower) and victim #4 (Central Mt. High School).
Assuming Joe didn’t know about 1998, which he testified he didn’t, how can he possibly be accused of being involved in a coverup?
Paterno must have known that, and apparently didn't do anything to stop it. I don't know that I would call that a cover-up, but it certainly seems negligent to me.