We indulge in genetic manipulation all the time albeit often unconsciously. For example, the spouse you choose affects the genetic makeup of your children. Whether you choose to have children in the face of a genetic disorder or whether you opt to use surrogate eggs or sperm is likewise a form of genetic manipulation.
With regard to using modern tools of molecular biology, my main concerns would be the ethics issues of the manipulation itself (i.e. whether the procedures involve great pain or death), a cost / benefit analyses (e.g. probability of risks to the child or the parents and the cost vs. benefits to society), and, perhaps more nebulously, what the common morality of the community accepts.
One major form of genotypic manipulation that is occurring in parts of the world is selecting the sex of the child. Historically, this has been done after birth through abandonment. More recently, it's been implemented via abortion. However, technology exists to select sex prior to fertilization. The prior two methods run afoul of many religious, moral and ethical proscriptions but it's not clear whether the last option is necessarily 'wrong'. In many cultures / countries with extreme preferences for male children, this leads to a skewed sex ratio that can significantly disrupt the society as a whole (Personally, I'd think the societies that favor one sex over another have fundamental issues bear addressing, but historically, that's a rather 'new' view).
But what would you say to a couple that has 3-4 children of one sex but would like to have one child of the opposite sex? It may be possible to filter for sperm of the desired sex. If the intent is not to intrinsically favor one sex over another but to simply aim for some sense of family 'balance', is that too much to ask?