Yes that is truly hard and i would have cried a lot about that when i found out. Society is getting better but large swaths of it still suck and HS can be one of those places.
Still, you should not let the actions of other small people dictate anything and you didn't and he didn't, that is integrity that is love, that is family. Everyone has burdens of some sort for sure. You contributed to his for a time but also you probably made him stronger and more zealous about his values.
Also, you and he paved the way a little further, for a world in which such mean prejudice will fade away.