Maybe not in a state sanctioned way, but it's still happening. There are several million abortions a year in this country and many more in the rest of the world. A good deal of these procedures are carried out because the fetus is abnormal in some way. It's only a small leap from allowing parents to terminate defective offspring or those of the "wrong" sex to allowing them to custom order desirable traits for their children. IMO, many governments will either play no role or a very small one in such decisions, and it will be up to parents to decide for themselves if they want their children to be specially designed or a throw of the dice.

As for your view that "enhanced" people will want to do away with "unenhanced" people as a means of keeping undesired traits out of their gene pool, I don't buy it. I believe another solution is more likely. Imagine if those who embrace gene modification choose to make it impossible for crossbreeding with natural people to occur. By altering the enzymes of their gametes, it won't be naturally possible for a union of a modified sperm and unmodified egg (or vice versa) to occur. In fact, once gene modification advances past a certain point, forced speciation will likely be enacted to help insure unviable offspring aren't conceived on a regular bases due to the genetic incompatibility of the parents. This idea may bother some people, but I'm not one of them.