Write or Wrong, your story is very sad and your son will always remember what happened. I can remember very clearly the awful lemuday kodesh teachers I had when I was young who embarrassed me in public. Boruch Hashem I was blessed with wonderful teachers later on in life.
Unfortunately this is how life is. How about kids who have been abused by parents and teachers. How difficult it must be for them. But as they grow older they hopefully understand that these people are mentally ill and are very wrong.
We must show our kids our love and support especially when experiencing such terrible things. And we must daven and say Tehillim for our children to have good role models and be surrounded with good people.
I am wondering if your older son who is off the derech had an experience that made him so angry at charaidi people. There is so much anger there.