A quote from the McCann article on SI.com:
There has been much debate as to whether the NCAA should punish Penn State, but it is clearly authorized to do so and could even impose the "death penalty," whereby the Penn State football team would be shut down for at least one year. Articles 2.4 and 10.1 of the NCAA constitution command ethical conduct on behalf of coaches and others associated with athletic programs, and 2.4 expansively states, "These values should be manifest not only in athletics participation, but also in the broad spectrum of activities affecting the athletics program."
This is the opinion of a law prof specializing in sports law. Notice the last sentence, which can make the entire "is it about football?" question (construed narrowly) moot.
Your questions about the application of these Bylaws in other situations are definitely a topic for discussion. I don't claim to be an expert on the history of NCAA investigations and sanctions, but the precedent seems to be that if you discover things and report them yourself, and don't establish a pattern of negligence or willful ignorance in letting things happen repeatedly, you get off free or with minimal sanction. The actions of a single bad actor don't constitute an Institutional problem, but the Institutional response can.
I would ask you a couple questions, before we start to drill down into hypotheticals of lesser scope (as this may well be a case of first impression):
Do you agree that the Bylaws in question establish jurisdiction in this case? If not, what scenario do you envision in which they would apply?
If you think they apply, do you think they should be enforced in this case?