I think the question makes some sense with Aristotle, given a lack of familiarity, since the ancient Pagans tendency to simply murder children born with birth defects is well-known. Not, of course, that the malformed were generally considered guilty of any moral defect (which is absurd), but the idea that they were seen as somehow be less worthy as people in various respects makes sense.
But even a cursory familiarity with historical Christian thought would make ascribing this position to Christian teleology impossible, I would think. The prohibition on infanticide was one of the most sweeping changes in the rise of a distinctively Christian culture, and moreover, it remains a live issue to this day.
So while I can understand the concern to the effect of “if x is better than y, doesn’t that support poor treatment of y,” historically, it seems misplaced to me. The eugenics movements tended to be highly secular, or even anti-Christian, explicitly deriding Christian teleology and views on the sanctity of life as malignant superstitions.
Even today, as the age of first pregnancies has soared in developed nations, defects like Downs Syndrome have been, in some locales, almost eliminated in live births. Of course, because of rising maternal ages, conceptions of trisomies have actually been increasing, and so this shift has been achieved by terminating otherwise wanted pregnancies precisely on the grounds that the disabled child is too much of a burden on the state or parents, or would lead a life not worth living because of their disability. And indeed, the arguments for infanticide in such cases tend to be entirely from atheistic grounds, with Christians and Muslims generally being accused of superstitious dogmatism on this issue precisely because they won’t budge on the equal dignity of human life. Hence, it’s hard for me to see where this connection even comes from, given the types of groups who have actually argued for the euthanasia, sterilization, or termination of the disabled.
Or, more modestly, it seems entirely possible to justify eugenics, bigotry, etc. on utilitarian grounds, and obviously on anti-realist and sentimentalist grounds, so that pointing out that teleology conceivably could be read in this direction seems to miss that this seems true of all the major theories.