Listening to your story certainly brings back memories with our son and the multiple physical setbacks. I feel your pain but I feel a strong sense of calm with the way you describe your/his scenario. It is obvious that your son is balanced and well grounded and will adjust well to these changes in life that will continue to present themselves long after baseball days.
Even with the support of the school and the best doctors involved, I know it is emotionally difficult. But, once a direction is chosen, the strong foundation you have provided your son over the years will allow everyone to move forward with proper perspective and a positive outlook.