RJM - I am sorry that your son was injured. I know it is tough. Teenagers were made with a mind of their own and so often then have to learn for themselves.
But I think you may still have good options available to you. Especially since your focus is on academics as much or more than baseball. I agree with what Bulldog 19 said much earlier in this thread. The bright side is that with your son having the injury now rather than a year from now it may help him focus on the more important things about his college decision.
How is his baseball resume? Does he have showcase results, newspaper clippings, or scouts that are already familiar with him? These are things that can be utilized to get colleges interested interested in him even with his injury. I suggest that you use any information you have to target the higher academic D1, D2 and even D3 colleges and I'm sure he will find a good fit.
Good luck! I've dealt with some similar issues.