If football is going to operate outside of the NCAA, then just go ahead and sever it completely from the universities as well, or at least those football teams that choose to. Just become a minor league, wipe the university's name off the uniform, and no more scholarships to said university. Just go ahead and get yourself paid like the professional you want to be.
No more LSU Tigers, Ohio State Buckeyes or Florida Gators. You're now the Baton Rouge Bengals, Ohio State Teletubbies and Gainesville Crocks.