sorry about the 'deleterious allele' thing.. you have to understand that it's along time since I studied such things and most of my genetic terminology is long since forgotten. Please also understand that I'm thinking as I go along here so please have patience if I say stupid things.
Presently I'm thinking that the problem isn't the faulty gene itself but the pathology it causes. For example, the problem with Phenylketonuria manifests itself in the lungs. Therefore, I'm not 100% sure that wiping any gene out is a good idea, (only about 99%
). Other methods to work around the problem would be just as valid as any tinkering with the genetic pool and a lot less open to issues of morality. Imagine being able to whip out the lungs and replace them with some other mechanical device which could provide the body with oxygen. In a senario like this, the existance of such a gene becomes irrelevant. What if the functions of the nervous system could be reproduced in some other more mechanical means thereby making Huntington's and other simlar afflictions irrelevant. Again, getting rid of the gene in the first place would probably be a good thing but, as you say, this presents so many moral problems in terms of eugenics etc...
Also, no matter how well we could refine our gene pool, wouldn't other genetic mistakes start happening? Some would be good and some would be bad as they are now?. Maybe the fact that we use such a fragile medium with which to pass our code on is, in some ways, a hinderance to further evolution???