The whole notion of growth being stunted by heavy lifting is a myth. It didn't do a thing to stunt the growth of Shaquille O'Neal, David Robinson, Karl Malone, Michael Vick, etc. All started lifting in their early teens, and all have gone on to be over 6' tall and star in professional sports. Dave Draper and Arnold Schwarzenegger started lifting younger than that; again, both are 6'1" or taller. Many high school teams start their freshmen on lifting programs, meaning your son started at a perfectly appropriate age. Your son won't find his growth stunted by lifting; rather, he'll find that he grows into his body much better and much more quickly than most of the people around him.
I'd also point out that the compression forces on your legs and spine are far greater in running and jumping than they will ever be in squatting.

Compression forces in running and jumping can exceed 5 times your bodyweight. If you're not squatting over 700 pounds, you're generating greater compression in normal daily activities.