There are issues with the way those are calculated. (about to get techincal) The basic formula is graduates/students. The NCAA doesn't use the Federal Graduation Rate because of issues with it. The FGR counts all students who enter the school as students even if they transfer out, but they don't count as graduates even if they graduate elsewhere. It does not include transfer-ins a students. Therefore you have to count transfer-outs as non graduates and transfer-ins don't help. The Graduation Success Rate that the NCAA uses doesn't count transfer-outs as students if they were academically eligible whether or not they graduate elsewhere. (Left-Eligible) It does count transfer-ins as students and graduates. The effect is that transfer students "move" to the new school. However, a student who leaves a school while eligible but never enrolls elsewhere isn't counted against a school's graduation rate. The numbers appear to be extremely high, but that is how the NCAA wants the numbers to look so the calculation is set up to ensure that the stated graduation rates are high.
That doesn't negate your argument. The schools do try to keep the publicly stated numbers up. They do push kids to go to class and get tutoring. (Though some do push easy majors, fake classes, and pressure profs to "correct" grades.)
I actually think a separation would be good for college athletics. You could have a minor league system "sponsored" by colleges, and then an association of colleges that compete against each other. If football does become a professional system at some schools, why would there be any academic requirements whatsoever? The teams could bring in players and cut them as they see fit. You could keep a player ten years or cut them after Summer camp. There would be a lot of argument over separations of conferences and money, but I think football would be the easy part of the split. I also don't see a professional minor-league system supporting lower tier sports. Where would the lower tier sports teams play? Would the ACC still let FSU play softball and volleyball as ACC teams if the football team is part of a professional organization? Forming the professional organization would be easy compared to cleaning up the mess it would make of college athletics in general.