The NCAA rules for ethics, supervision/control, outside agencies, and illegal activities that you quoted are all in relation to following the NCAA rules. Example, it is against NCAA rules to have an agent. If the school allows a school to have an agent, then they broke the supervision rule because they didnt report an NCAA violation. If a person witnesses a crime and dont report it, it is against the law, not against an NCAA bylaw.
And yes, PSU accepted the sanctions, but they did not have much of a choice. If they went to court, I beleive they would win against the NCAA, but going to court would drag this out and PSU clearly wants to move forward, hence just accept the sanctions. Im honestly not even sure you can go to court on something like this, but if you dont accept, you are out of the NCAA so what choice is there really?