That may have been the stated reason for the NCAA's doing what it did. And the graduation rate is a legitimate concern. But what they did hurts players without helping to solve the problem, or even to make any improvements at all.
The NCAA also needs to remember that all sorts of college students transfer every year for all sorts of reasons. Of those, only athletes in football, basketball and baseball find themselves barred from their chosen extra-curricular activities for a year. For football and basketball, at least you got a full ride in exchange for this proscription. To impose this on a baseball player who might be getting no more than 25% and who, on average, is getting something like 41%, is overbearing.
My daughter majored in musical theater. Imagine that she had transferred, only to find that she couldn't be in any theater productions for a year. Crazy, right? Now change "daughter" to "son" and "musical theater" to "baseball" and tell me how it makes any more sense.