WOW, your job is to be a parent and to protect your children! Just because this guy knows how to learn, that doesn’t mean that he is applying his learning to real day to day life. Where does it say in the Torah that he has a right to hit someone else’s child?
Just because your RAV is afraid to speak to him, and just because your RAV didn’t tell you to go to the police, that doesn’t make him right either. Did he tell you NOT to go to the police? If he didn’t tell you NOT to go to the police then the choice is still in your hands.
It is NOT your concern whether or not the police love this kind of thing. This man loves this kind of thing, going around forcing his way of thinking on others. This is NOT chinuch, this is bullying. A True ben Torha, who wants to teach kids Torah, would go over to a young boy and say “Excuse me, tateleh, may I have a word with you? It pains me to see bochurim acting in such a manner not befitting the kovod of Shabbos. You probably didn’t realize that you were doing something that was not kovodik to Shabbos. I am sure you didn’t realize, but throwing rocks is not something that one does on Shabbos because…….The Gemara says……Do you have any questions about this? I will be happy to learn the sugya with you or answer any questions you have about this inyan. I see that you are a fine boy and you wouldn’t do anything to desecrate the Shabbos, so I felt a need to come and let you know about this. Have a good Shabbos.
That is how a true Ben Torah would handle such a situation if he wanted to give Musar or tochecha. That man was nothing but a bully, and he deserves a taste of his own medicine. Your job WOW is to make sure your children grow up feeling loved and cared for, and know that what they learn in Yeshiva and in your home applies to them and every other Jew.
Maybe you should call all the boys to a meeting, both the younger boys and the older boys and let them know that it is your intention to go to the police and they would have to go with you as witnesses and give their statements. Why not to them as a group. In that way, you will ease your son’s embarrassment in front of his friends because YOU are showing ALL of them that this man was a bully and he did NOT represent TORAH in any way shape or form, and that you are willing to prove it by going to the police. You are also showing that to your older son and his friends. If your Bar Mitzva boy decides to go to the police then do it. If he decides to let it go, then say “OK, I will let it go this time, but I will let him know that if he ever comes within 5 feet of you again I will call the police on him. Maybe even consider getting a restraining order against him to keep him away from your son.” And then follow through. Let him know that since he didn’t think he did anything wrong, and he didn’t apologize, if he ever goes near your son again you will call the police.
I believe this will help both your sons have a different perspective on things.