I'm not sure if I would bother. The mold might not go during seasoning and there are likely other things causing the spalting--a few kinds of fungi, e.g. Whether or not if would affect the flavor I don't know. I think the possibility is there, especially if the spalting is significant.
I dson't know how common spalted wood is in your area but you might want to see if there is a woodworker or wood turner that would be interested in it.