WOW, his “disease” as you say is that he is angry at religion. Unfortunately he feels that he was hurt by the religion and NOT by religious people or people who represent the religion. I have often pointed that out to children I have worked with in the past and even asked the very logical question “so then if a goy would hurt you would you then turn your back on all goyim , their music and everything they believe in because that would mean they are all bad and everything they believe in is bad and harmful to you?”. This usually caught them off guard and gave them food for thought.
I don’t know if your son is capable of hearing that question at the moment but it is an important question to ask because one must define why one is hurt and angry and who is responsible for it. Yiddishkeit is no more responsible for the way he feels, than the air he breathes is. The people in in his life who were frum and let him down are responsible and they have names and faces and they didn’t hurt him because they are frum, they hurt him because they have the power of choice just as he does. They chose their own actions just as he is doing now. That doesn’t mean that it was the right choice at the time nor does it mean that they followed religious guidelines when they made them. It means they are human and as humans had the choice between right and wrong, good and evil just as he does, you do and his friends do. religion does not play a part in it whatsoever . One day when they stand before their maker they will have to account for their choices just as he will and you will. Hashem keeps very precise records and everyone has their day of reckoning.
This is an important message that kids have to hear. They have to understand that people ,no matter how religious they are or seem to be, still answer to Hashem and account for every person that they hurt throughout their life just as every secular Jew or any regular joe shmo. We are all on equal footing in front of Hashem and it is our record that has to speak for us.
Although you can’t catch him to have a chat with him, there are two other methods to get your points across to your kids. One is since kids rarely appreciate their own parents and think that their friends parents are cool and smart, have THEM tell your child what you want him to hear. The second way is to leave him notes. Kids at this age show tremendous bravado face to face but in private they let their guard down. If you write him a sincere note he will probably keep it and reread it many times. Make sure to be warm and loving. Make the notes short and sweet but get the message across. Leave it on his pillow to be found when he comes home. Be sure to seal it so his siblings don’t read it. Respect goes a long way, if you seal it you are showing him that you are teaching his sibs to respect his privacy. Hatzlocha Rabbah.