I used to be a competitive amateur golfer but then in my late 30's developed the "Y" wordwhichshallnotbenamed when putting. In a tournament round once I hit 13 greens in regulation and three jacked 8 of them. Pretty embarrassing. Everyone knew what was happening. It was a tough thing to overcome. I went to cross handed putting, big grips, long putters. Quit playing competitively for awhile. It is an interesting phenomenon. Usually occurs when people get fairly accomplished at something after many years.
So for a young kid, I think he can overcome it! I bet he doesn't have the problem when he is really active. Usually happens with fairly stationary acts like putting or free throws. Similar to what Dmac said: Have him work on a set routine that he will use when he throws back to the pitcher; in addition to what he said, maybe: pop the glove once so his hands aren't static and shuffle hard; point shoulder at target and GO.
It helped me to not give a flying F about my score or what anyone thought of me. Ultimately though, grooving my routine so I was process oriented instead of results oriented is what resolved it.
Good luck and many positive thoughts your boy's way.