Given that researchers still don't know what causes autism, it may have a genetic component. Therefore the island may not see Daniel's condition as a disease, just like it wouldn't see shortness as a disease and make someone 'normal' height. I tend to think Daniel does have a connection to the island. He reminds me of:
http://en.wikipedia.org/wiki/Temple_Grandinwho designed humane fencing for cattle (Svetlana!) at slaughterhouses. Dan's makeup allows him the singular ability to see the special nature of light on the island, which others can't. Will he lose these abilities if healed?
But like Juniper Jade says, Charlotte indicated that Dan is getting better. Unless that's purely consolational, the island seems to be partially/slowly healing in this case. Why?