There is more to the low rate than just the draft. The draft might lower the rate 5-10%. A TV talking head, Tony Kornheiser I think commenting on the BCS said the biggest crime in college athletics is the college baseball schedule and its affect on class attendance.
The fact the kids load up Thurday or Friday and get back Sunday night or Monday morning 12-14 weeks in a row doesn't exactly pump up that GPA. They can and do study on the bus/plane/train. That said, the kids that want to graduate certainly have that opportunity. imo, I think graduation is a personal choice in most, but certainly not all cases. Some kids, playing baseball or not are without the ability to meet the requirements to graduate.
Without baseball alot of kids would not likely take a college course at all, Stanford players and many others excluded. Are those guys better off than if they never went? Probably they are.