Julian Sanchez is quite right about this: If you support the blanket legalization of abortion, there's really no reason to find the abortion of embryos and fetuses with genetic defects any more morally problematic than the abortion of embryos and fetuses for financial reasons, or personal reasons, or almost any other reason you care to name. If anything, as Julian says, it's arguably less morally problematic:
I am supposing, for instance, that as self-identified pro-choicers, they're not raising a fuss about abortions had on the grounds that a child would be too disruptive or economically draining at some point in a woman's life. Why are these very reasons suddenly suspect if instead it's that the added difficulty of raising a child with a serious disability would be too disruptive or economically draining?
Julian suggests that this is "a case [where] people are vaguely uneasy about something that seems analogous to various other objectionable things," - i.e. Nazi-style eugenics - "but where in fact the analogies break down precisely at the points of objectionableness." For my part, I like to think that people are uneasy about the practice because they understand on some fundamental level that abortion is wrong, and killing a fetus because of something particular to its nature, rather than something particular to the mother's situation, throws the wrongness into relief - by serving as a reminder that a fetus is alive, with human qualities, and that in killing it you're killing a creature rather than a thing.