atheism can be better than cultism, but they can be more hateful towards believers...
i'm assuming he's probably young if he's still in school, it's a good time to try new things out, spiritually...the insults can be a normal thing that come with school age children, my daughter is subject to them being slightly different than the other children and they definitly have gotten more cruel out of elementry school into a middle school....and high school is even worse.
it seems you're putting too much stock in his faith, dismissing issues he's having on a personal level, sadly there's not much you can do, show him by example, accept that he's going through changes, be there if he needs you and you want to be there for him, but generally it's hopeless trying to change him, when he's obviously going through so many changes himself...and will probably spend a significant amount of time doing so.
be a friend to him in so far as you're not opening yourself up to cruelity but this is an issue he has to resolve for himself, God may try to intervene but i've found He seems to prefer people finding Him through their mistakes, willingly embracing Him having learned what they need out of life versus what they want and deciding what's best to support their needs.
some people have to make their own bed and sleep in it before they realize where they're messing up, otherwise you'll always be their maid.