The issue with the "unnatural" argument is that it is really not a good argument to refrain from something. Ventricular Assist Devices are certainly pretty unnatural, and in earlier times the idea of transplanting organs would have been seen as violating the natural order. These are obviously worthwhile technologies in spite of that unnaturalness.
Citing overpopulation as a reason to avoid developing a medical technology is also pretty silly. The main problem when "overpopulation" is cited is actually the expected shortage of certain resources and the quality of life reduction that would follow, not the number of people in itself. Thus, trying to limit population growth by imposing lower quality of life via halted scientific progress solves nothing.
That being said, I'll reiterate my agreement that playing with our genes in this way should definitely be limited. This is because we really don't know that much about the long-term ramifications of tampering with our DNA right now. We could really fuck ourselves over and make ourselves too genetically homogeneous if we tamper our genes too aggressively. However, even if we did know what we were doing, if we didn't just focus on fixing the objectively nasty stuff and instead tried to push for better, less disease-prone humans, inevitably some births would evade the screening process and bam, we would have a new, man-made, "scientifically proven" reason for people to be dicks to each other. I'll bite the bullet and say that this means we oughtn't implement a process by which, during prenatal development, we would screen for and alter genes that could encode for, say, elevated cancer and heart disease risks later in life. The can of worms that opens is just too slimy and nasty to be worth it, imo.