As in many cases, the original OP is asking a question which already exists - the condition is known now as intersex and has never worried the Christian community very much because it is simply too complicated. 1 in 2000 births are born with ambigious genitalia. 50 years ago they used to believe that it was environment that created gender identity so they actually had a ruler and if it Y long, then surgery would make it a boy, and but only X long and the genitals would be cleaned up to make it a girl. Of course, months to years later, when the gender identity starts appearring this was often at odds with the "assigned" gender resulting in adult corrective surgery or suicide. A famous example of this line of thought and the outcome is David Reimer:
http://en.wikipedia.org/wiki/David_Reimer
As for the chomosomically opposite gender, this particular condition is called AIS or Androgen Insensitivity Syndrome: means that the body is incapable at some level of absorbing the hormone androgen (males and females have BOTH estrogen and testosterone/androgen in their bodies, just in differing levels, androgen is the dominant male hormone). What this means is that a sperm and egg meet, making an XY combination, the DNA creating small testes. However, because androgen cannot be absorbed (this is an inherited condition 66% of the time) the fetus follows the Eve Default, because all fetus are female, it is the washes of hormones and the changes which subsequently occur which make males. Thus, when a baby with Complete AIS (CAIS) is delivered, there is a normal healthy girl. The girl, complete with appropriate genitalia, will not have a uterus or ovaries, but rather internalized testes, along with an XY chromosome instead of the XX chromosome. The girl will develop normally through puberty, including breast development but without menstruation. It is either now or later that a doctor will be consulted, who with a consult to an endocrinologist, will determine the CAIS condition; which is usually followed up with a recommendation for removal of the internalized testes as they can become a significant cancer risk.
Unlike the "assigned" genders of the 60's onward, CAIS females, do not have gender identity problems. They know they are female, everyone knows they are female. It is only when the XY chromosome normally associated with males becomes known that ignorance in society starts imposing their binary preconceptions (if you think gender is only determined by chromosomes you can give yourself a wake up smack now; if you are a Christian and use the phrase God doesnt make mistakes to justify this view, find yourself a really big bible to smack yourself with).
Traditionally doctors have lied to their CAIS patients, often removing the testes under the guise of removing problematic ovaries, or simply saying they have a uterus problem and cant have children. Of course, when the patients found out later as adults, THAT caused psychological problems. Indeed CAIS used to be called Testicular Feminization (tell me you cant hear the male oriented panic in that term). As regards to sexual orientation, one CAIS female reports that lesbians occur about 10%, the same percentage as the general population. But only ignorance places CAIS as anything other than females, they just happen to be an XY female. Indeed, It was because of conditions such as these that the Olympic committee dropped the chromosome test qualification in 1990, simply because 1 in 400 women were getting negative results; and having to face the media storm of its a man! before being cleared by doctors as females (ALL females competitors who tested negative in recent Olympics were cleared by doctors as females). Some competitors, after the initial negative test results were so traumatized, that they dropped out of sports entirely (like sprinter Eva Klobukowska who had XXY chromosomes; another intersex condition).
There are about 16 different intersex conditions. AIS is merely one of them. Some CAIS women are already married and adopted children before they find out thier condition (remember the doctors that told them they had a "bad uterus" and removed the testes) - there are equivilant intersex conditions for gender identified males, I know one who is a minister, and has adopted children, been in a marriage for 30 years and though the only testosterone in his body comes from an injection and his chromosomes may or may not match those of other "men" to somehow try to make his life into "gay marriage" would merely be a display of ignorance. First off, the term "gay marriage" implies a sexual orientation - and simply this - there IS a different between gender identity and sexual orientation. When you wake up in the morning you expect when you look in the mirror to see a) a male or b) a female - this is your gender identity. If you expect to see A and you see B reflecting back - then you have what is referred to as Gender Identity Disorder - go see a doctor and they will refer you to a specialist to determine whether this is a result of a pre-existing intersex condition, a transseuxal condition or a side effect of another condition (for example other diseases can produces this feeling as a side effect, specifically Schizophrenia).
Sexual orientation is who you are attracted to (people like Johnny Depp and Angelina Jolie excepted, who seem to be attractive to both sexes) - if you find yourself interested/aroused/wanting to share your life with a) someone of the same gender identity/sex then this is referred to as being "gay" - thus "gay marriage" is one between two people of the SAME gender identity. Unless of course Christians again want to ignore thousands of doctors and the olympic committee and make some sort of pronouncement that while simplifying the world for them, makes pain and havoc for others.
The main concern for doctors with intersex, ambigious genitalia and other similar conditions is for the welfare of thier patient - history has shown that this is BEST served by matching the gender identity of the person to the body (which is why many doctors wait a few years after birth before doing any surgery) - simply doing a chromosome test and chopping and constructing an outcome IS not the best solution (especially since two rare intersex conditions create bodies that produce both the XX and XY chromosomes from different parts of the body - I guess we cut them in half? Also, there are 6 people currently alive who have BOTH fully functioning genitalia).
Medically and historically, diversity WILL occur in humans, and DOES already - it is simply that most people are unaware of these and other condition, and in that ignorance, may make assumptions or say things which are bigotted or emotionally harmful.
In an aside, India has already aborted 5 million babies based on gender (female) and created a new test to tell the gender of the fetus earlier on; also Dr. Charles Rosselli of Oregon is already trying to alter fetuses of sheep to turn them from gay to straight - with potential human applications.
