First welcome to the site and you will find a ton of people on here who had sons in the same situation. Very knowledgable people will be along later with tons of advice and stories to let you know it's not the end of the world.
My first bit of advice is to read this
http://joshherzenberg.blogspot.com/This is a blog chronicling the recovery process of our very own JH who is a college pitcher. You're going to be very impressed with all aspects of this young man's blog - from the high level writing, to his knowledge of baseball and all kinds of things.
My second bit of advice is to really not change that much from the original plan of recruiting. Keep contacting schools that your son is interested in. They understand these things happen and it's no longer like it was 20 years ago when this was an end to any career. He may not get a scholarship out of high school but he may get a spot and work his way into one once he proves he's healthy.
I know you and your son feel like he's in this tunnel but understand the light at the end of the tunnel isn't a train heading at you guys. There isn't a guarantee it will work out but the chances of it working out are pretty good once he gets to the rehab. The rehab is the most important part because if he can't get healthy then there's no chance of any scholarship or spot on a team.