RJM,
Gotta be tough on RJMjr...been following him and sis for a number of years on this and another site.
You know about all the injuries my son had his Jr. and then Sr. years (knee then broken collarbone). All I can recommend is doing what he did and keeping the nose to the grindstone by doing the surgery,rehab and whatever type workout is possible. Keeping all the coaches in the loop after you get the diagnosis/prognosis is equally important as they have seen alot of kids go through this no worse for wear. Personally, I've seen several players come back better than before due to an improved attitude and the realization how much they love the game.
JUCO is a good option in our area but may not in yours. Still something to consider if need be; good chance to get the required courses out of the way and still play baseball.
While baseball may be an avenue to a scholarship to college, if they don't come about due to injury so be it. If your son wants to continue playing in college, then walking on is an always an option. A tough option for sure but perhaps the only one available initially. It's the route my son is going to have work through...he won't be the first or last kid facing the climb.
Really hate this for your son; seeing a gamer sidelined is sad.