A child is not the property of their parents; it is not a thing with which they can do what they want, using it as a 'mere means' to the fulfillment of their interests. Like any human individual, each child is to be regarded as an end in itself. Many of the ethical issues surrounding reproductive technologies occur because they encourage or reinfornce unseemly or repugnant attitudes towards the worth of human persons, that run against the proper norms of parental love and devalue children (see, for example, discussions regarding commercial surrogacy). The fact that a child is not the parents' property also sets important limits to the value that can be accorded to parental choice in this situation; basically, you can do whatever the hell you want with yourself and other consenting adults, but when your choices affect other non-consenting individuals, the moral alarm bells will be poised to ring. No decision made by parents with respect to their children is 'no one's business except the parents'; the state has a duty (and the right) to protect the interests of all children within its juristiction.
So what is wrong with choosing the sexuality of your child? Firstly, there might be many reasons for choosing a child's sexuality that I find to be relatively defensible. For example, (though I find even this somewhat problematic) parents might wish to spare their children the horrors of homophobia (this is problematic because it would, if widely practiced, be tantamount to 'conceding defeat' in the fight against reprehensible prejudice; it would be 'if you can't beat them, join them', and we certainly don't want to join them); also, gay parents might wish to have gay children, and mutatis mutandis for heterosexual couples, because doing so leads parent and child to share roughly the same world of experience, the same problems and joys in relation to sex and relationships.
My major concern is not really with these choices (I would tentatively suggest that the second kind of choice is entirely unproblematic), but rather with those born of homophobia; the sort of parental choices highlighted in the article. When a parent selects against their child being born with a certain sexuality based on the fact that they consider such a sexuality reprehensible or defective, they are not treating their children as ends in themselves, beings worthy of love and respect, for their love is being tagged as conditional on their obtaining the right sexuality. A child who grows up knowing that they had been 'saved' from their homosexuality will always wonder what their life would have been like had they been born before the advent of such technological advances; would they not then have found themselves repudiated and derided by their parents? In what sense, then, are they truly loved by their parents, if that love could turn to disgust so easily?
Allowing parents to 'heterofy' their children would be a reprehensible decision, I feel, because it encourages an attitude towards the worth of children and the worth of non-heterosexuals that is quite simply incompatible with proper parental love and with a decent, egalitarian society. All-out homophobes - and there are so disgustingly many - would use such technology to root out homosexuality in their own offspring, thus furthering marginalising gays, lesbians, etc.; entirely decent people would too often be moved by sympathy for their child-to-be and seek to heterofy the child so as to spare it the horrors-to-be inflicted by homophobes; and thus, homosexuality would quite probably become 'weeded out', further marginalising the gay community and empowering those who wish to see its members defiled and humiliated.
Consider an analogous situation. Imagine that we are living under conditions of terrible racism. Blacks are derided and hated by the majority of society; the Conservatives have no shame in publicly insulting them; there is a wide and popular movement afoot to make it impossible for blacks to marry whites, etc. Now imagine a piece of genetic science-fiction, such that in this society blacks are sometimes born to whites and sometimes to blacks. And now, imagine that someone has discovered the genetic (or some ontogenetic) condition for black skin; the Conservatives rejoice, for now they can make sure that they do not have black children. Decent parents are now given a means by which to spare their children the horrors of growing up black under such awful conditions. What would happen in such a situation? Would it be desirable? Most assuredly, it would not.