In the past 24 months, my kid has had 4 MRIs: Severe Hip Flexor Strain, Grade 1 Ulnar Collateral Ligament Tear, Shoulder Labral Strain and possible Hamate Fracture. (Still waiting on the results.) So, I have some experience on this topic.
As a parent, each time, I just reminded him that he's still on the team and this isn't a reason to check out. Go to practice even if it's just to pick up balls in the batting cage. Go to games even if it's just to be a cheerleader or count pitches. Personally, I feel this is important because it makes the kid see what they are missing and helps keep the eye on the prize of fighting to get healthy again and back out there.
Years ago, a friend had a son who was very highly touted as a pitcher in High School. College and pro scouts were sniffing. He hurt his arm and needed surgery. He was totally out and took that time away from the game. While absent, he decided he was having too much fun with his girlfriend and decided not to play baseball anymore.
I wasn't shocked. Absence makes the heart forget.
On the mental side, each time my son was hurt, I kept stressing to him to stay positive, not fall prey to any fears that he couldn't come back and to focus on what he needed to do to get back on the field.
The worst part sometimes is the "I know a kid" thing. If your son has been playing long enough, he probably has a network of buddies in the game. And, it seems that everyone has had something at one point with many associated horror stories. In this situation, a kid is sometimes convinced that he's going to suffer because he knows a bunch of guys with the same thing and they had a terrible road to travel when they had it.
That's another thing that you have to help a kid navigate and fight against. Not every situation is the same.