Academics should DEFINITELY come first...But I feel like in your son's situation he chose a school where he has still established academics as his top priority in that he is going to a good school while at the same time fulfilling his criteria in other areas. I think there is a difference between using athletics to get into the most prestigious school possible and going somewhere that suits your son the best while at the same time providing a solid education. I think he made the right choice. In my mind problems only arise when a kid goes to a school that is below where his academics dictate he should be just because a school is offering him the college baseball opportunity.
If you don't mind saying though, what top academic school offered him and what school did he end up picking?