S.H.
I am a grandma and a teacher so I can empathize with both you and the school. Here's an idea that might help. Perhaps the teacher might let your son "invite" one or two friends to lunch with him at the end of the table, rotating each child in the class so no child is left out. The children will receive their invitation (along with a list of specific foods that cannot be included in the lunch box) the day before. If it is presented as something special for the children to do, it will be like a privelege and evoke excitement in the class.
If bringing a lunch from home is a problem for the invited child, perhaps you could send a second lunch for the invitee. (I assume you send lunch from home for your child) This would prevent the isolation of your child at lunch time. It might also give your son an opportunity to cultivate friends he might not ordinarily have.
S. S.