smithers
I was in the same type of situation as you with my son. He was a 4.6 GPA out of 4, 35 ACT, and valedictorian of his graduating class. He was rated a 7.5 at 2 PG events to give you an indication of baseball abilities. He is playing baseball in college. He received plenty of academic money from the school.
It sounds like your son owes it to himself to see what possibilities are out there to combine a good education with his pursuit of playing ball. It doesn't have to be one or the other unless in the end coaches don't believe he has the ability to play or he does not do the research to find the fit. But to find out those answers it does take work, alot of work.
To TPM's point I don't know what your son has done to fulfill that goal or attempt to combine good academics with baseball. For my son it was alot of college camps, showcases, playing for a top summer and fall team at scouted tournaments, contact emails and videos. This resulted in several offers to play in college ranging from D2, D3,JUCO, NAIA.
One of the schools, D3, had everything he was looking for from very good academics, his intended major, location, to liking the coach and the baseball program. That is where he is today. But I would be lying if I said it was an easy process. If your son has the ability and really wants to play he could find that fit. If he does not want to give up the big name school for academics for a college/baseball fit there is nothing wrong with that either.
I read a post on this site a year or two ago where a Dad answered the same question. He said he still wasn't sure if his son made the right choice in not going to the high profile academic university to go to play D3 baseball at a very good school. He knew his son made the right choice when he saw his son on their spring baseball trip in uniform warming up with the rest of his team. He was a college baseball player, something that completed him as a person.
It sounds like your son owes it to himself to see if that "fit" exists. And then make a final decision based on those options once they exist.