Thank you so much for your suggestions. I will definitely explore online options out there. AOPS, EPGY, CTD all sound great. kcab, your kids are lucky to be in such an appropriately challenging environment. I don't think DS's school knows what to do with highly gifted kids. They have gifted programs but they don't have many kids like DS. The principal said she had seen a kid like him before, but not recently.
Besides the problem of having to travel back and forth between two schools, he is emotionally and socially not ready to be part of middle school. For example, he will not understand the social context of many of the word problems they give him. He might also be vulnerable to teasing or bullying since he will not really belong in middle school. I am getting worried all over again just thinking about it! I hope they will let him do an online course by himself.