Sorry to hear this, best of luck to your son and him getting healthy.
Here's another perspective he should seriously consider. There is more to life than baseball.
My son played for 4 years, was injured and lost most of a season, came back and finished and had a nice Sr year. He went on and got his masters (fully paid because of summer internships) and now has a nice life working for a rapidly growing tech company.
He enjoyed it but has completely moved on without baseball. It happens to everyone at different times and while he may have trouble making the decision now, it might be best for him to move on with life. The fact is that most kids don't play for 3-4 years of college ball for a whole bunch of reasons, injuries included. Just another perspective, and best of luck in his decision.