This is simple. Why would you make drinking while pregnant illegal? Because it can cause birth defects, but is not 100% guaranteed, and the effects can range from uneven ears to full-fledged deformations or infant deaths.
Now, what if someone with genetic disorders wants to procreate? You know they have a 50% chance of passing it on, and if their mate has a similar disorder, as people seem drawn to others much like themselves, the risk increases. Can you tell them they can't have a child because they have a high risk of creating a child with deformities?
Of course, the other precedent is that some people who have had past issues may still cause issues with their baby even if they have stopped now. And since we are worried about outside influences creating problems do we also outlaw smoking, eating fish, eating fatty foods, walking through industrial zones, working in industrial facilities, etc. How many harmful to the fetus things can we outlaw? Where do you draw the line between negligence and lifestyle choice? A woman puts the fetus at additional risk the moment she gets out of bed. Can we mandate 9 months bed rest?