I just make one simple argument. Graduation with Obama as speaker turned into a public fiasco on campus, taking away from the significance of the event itself, becoming bigger than the event itself. Knowing that the current Trump controversy level dwarfs what Obama was dealing with at that time, it's very reasonable to think that will happen again, likely to an even greater degree, and maybe even to a much greater degree. The priority IMHO is to protect the dignity of graduation for those involved; the students, the faculty and their families. The priority is not to stand on tradition, even if it started with George Washington. Your priority is basically the heck with graduation and the graduates, honor the tradition. I don't agree.
You want to believe that this is indicative of some big picture evil scheme on the part of the ND administration to dishonor that tradition for political reasons, hence your #1 thru #4 above. You don't consider the possibility that it might have absolutely nothing to do with any of that. It might be simple pragmatism in the face of knowing what was likely to happen to graduation day if you invited Trump, and the administration having different priorities than you do.