What a great debate! Never one to pass up an opportunity to throw more gas on the fire; in my opinion, there is just no way that academics ALWAYS could come first, EVEN when you are going to college. The baseball window just isn't open that long.
My oldest is now at a four year school and a junior majoring in business systems. He is a very good student and will likely graduate at the top of his class in four years. Out of high school, he had three options; "Invited walk-on" at a mid level D1, signing for a small scholarship at a nationally ranked Juco (where we thought he had a good chance to play right away), and going as a "regular" walk on at in-state school.
When we looked at all of it, it was actually a pretty easy decision; we chose the juco because it was near home and he figured that if he was going to play higher level ball right away the juco offered the best opportunity. Does it mean that we neglected academics? Maybe in some ways, but our thinking was that his baseball "window" was open for much less time than his academic window.
It might have been different if he wanted to major in engineering, I will grant that, but he was a smart kid with some baseball ability that wanted to see how far he could take it. It is also very fair to say that most of our college decisions have been baseball decisions. If your son can decide that it is not "one OR the other" but "one AND the other" I don't see a problem.