I think you made the right decision. If it is hurting and he is feeling self-conscious about it, he should stay home.
If it was my daughter, and it wasn't bothering her physically, I would have sent her, though. I have been pleasantly surprised at my DD's school that the kids don't really tease each other much about stuff like that. Hannah went to school yesterday for the first time with glasses, and I think most of the kids were jealous of her.
Denae