Let me start by saying I know absolutely no facts regarding the School Disciplinary proceedings or what is going on at the CA office. But based on all the posts a couple things come to mind.
First, from everything published, it seems like a decision on the School issue has happened or going to happen in the very near future. It is possible that the decision was made and came out against JJ, hence he left town to decide whether to stay and move onto the Court or transfer. My question with that is that it would seem to be difficult to simply transfer if you have just been expelled from another University. Is it possible that the School has indicated that if he transfers it will suspend the disclinary proceedings so that he can transfer without an expulsion on his record. In fact, I have wondered whether his attorney has approached the University with such an agreement. He clearly has the opportunity to play at just about any FCS school he wants (and some FBS schools), but many of those opporunities may not exist if he has an expulsion on his record.
Second, as for the CA, it is true that whether to charge is solely in the discretion of the CA and not dependent on what an accused wants. However, without clear physical evidence and good circumstantial evidence it is highly unlikely the CA would bring the case if the accuser has indicated that she would not willfully testify. I doubt the accuser in this case has made any indication in this regard. If she (through her attorney) has told the CA that she would not want to pursue the case if JJ transfers, that would likely be enough for the CA to fold the whole case. Since it hasn't, my guess is that she has not made any such offers.
Third, I think many of the posts on this board confuse the ongoing criminal investigation with the School discipinary proceedings. While clearly one (criminal charges) can lead to the other (school discipline), School discipline is not dependent on on the first. My guess (notice the word I use) is that the school decison was based on more than simply an alleged crime. It likely found violations of other provision of the honor code to hang its hat on and that will likey not change. Myself I would not want to hinge my future on some academic (Commissioner of higher education) going against the School and its president. I think it would be wise (if possible) to resolve the school issues with an agreement to transfer (if such an option is available) and then wait to see what happens with the criminal proceedings. It doesn't matter if you are enrolled at UM, PSU or anywhere else if the CA decides to charge. Wherever you are your football career is going to be put on hold but if you stay at UM it is likely completely over regardless of the outcome.
Again, just a guess, but my guess is that JJ is either (1) deciding whether to transfer in exchange for some type of an agreement on a favorable resolution of the School proceedings and that it is not related to the CA proceedings or (2) has received unfavorable news and is deciding whether to transfer or go to Court to overturn an adverse ruling from the CHE.