A lot of people mature early. It sounds like your son has. His penis probably will not grow further.
Now remember that the penis is basically a muscle and while he has a size already genetically embedded, which he obtained from his mother's side of the family, exercise is what makes muscles larger, so yes it can during the growing years.
There may be an operation that can shorten a penis but what male would want to take chances with that.
He will need to learn how to control it, if you can educate him on how to not hurt a female. And then there are many women who not only desire that size, they can take it.
This is a unique case. Masturbation does not lengthen penis. I have not come across any method to decrease the length of the penise.I hope some one knowing the answer will reply to you from this forum.