The genetic risks that you mention that are associated with incest are not as high as society would have you think.
This link mentions that if we should pass laws governing sex based on genetic risk, then we should disallow sexual intercourse between the elderly, between those with common traits for genetic diseases, as well as between genetically similar groups (for example, between Ashkenazi Jews or Safardic Jews). And why not make genetic screening before having children mandatory while we're at it?
I believe that incest, homosexuality, and polygamy all suffer a stigma brought on by the bible and that the laws were written because of this stigma, and not for any rational reason. Yes, it would be better for society as a whole if certain people didn't have children, but do we really want the government to tell us who those people are?
Even if one were to say that we want the government to control who can have children and who can not, I would like to point out that in today's day and age, sexual intercourse does not have to have a significant chance of impregnation and therefore should not be outlawed under any consensual circumstance.