Lets get the usual arguments out of the way...
"There's no such thing as a gay gene because the bible says being gay is an abomination" and "Homosexuality is a choice"
That being said lets talk a little bit about the reality of such a conundrum. I suspect that even though the vast majority of fundamentalists will agree that the worst thing you can be is a homosexual (whether born or not), the worst thing you can do is kill an unborn baby. To that end I would expect things to proceed pretty much the same as they always have: allow the baby to be born and then persecute for being gay it until it is old enough to commit suicide, then blame it for living a vile-lifestyle. Having a prenatal test for homosexuality doesn't really change things for fundamentalists since in their pea-brains the bible supercedes science even when science clearly disproves the bible (science is the Devil, evil, liberal, etc.)
For the more rational set (read: liberal theology, liberal Christianity) the discovery of the process whereby a homosexual is created prior to birth could be easily assimilated into their worldview. For them (and myself) the past OT conditions that made homosexuality an "abomination" don't really apply to non-ancient-Hebrews and the supposed NT condemnations of homosexuals are clearly the result of a blatant mistranslation. Of course if you do believe anal sex is a sin there's still no need to be dogmatic. Afterall even if it can be demonstrated that a person is genetically programmed to be the "world's most flaming queen" if they never have anal sex, they'll never have a problem (harassment and teasing maybe).
The biggest problem I could see is that when this test becomes availible it won't be the fundamentalists (who abhor abortion) or the liberal theology crowd (some of whom might actually get a kick out of having a gay son or daughter) who will be using it to screen fetuses. Its going to be the ones who want the "perfect" child and for whom a gay child just doesn't fit in with their view of the way it ought to be. That sets off alarm bells in my mind because if they can do that how long is it going to be before they want only pro-athlete, nobel prize winning, supermodel children? Has anyone else seen GATTACA?