First, there are many behaviors that outside the context of Christianity may be amoral, but within the context of Christianity are to be considered immoral by those who have chosen to follow Jesus. I believe that it is immoral to use violence against your enemy. I also think it is immoral not to pray for your enemy. I think it is immoral to ignore the plight of the poor, swear oaths (still fuzzy about this one), get drunk, lie, defraud, gossip, horde wealth, lust, covet, etc. I do not expect that a person who is not a follower of Jesus should hold to the same moral code.
An example (probably lame)...
When I challenge a believer who has abundant wealth to consider giving some/most/all that wealth away, I will usually share my conviction that amassing wealth for ourselves is morally wrong. I do not think that reveals a prejudice against wealthy people, but rather what I consider to be moral behavior for a Christian.
I would not expect an atheist to hold to the same moral code about praying for your enemies...what sense does it make? Furthermore, the fact that I think it is a moral obligation for Christians to pray for our enemies, doesn't require a prejudicial attitude against atheists who don't pray.
I think the same could be said about homosexuality. I would not expect a homosexual who is not a believer to practice the same code of morality, and I certainly wouldn't try to legislate that morality code and make them live by it.
Most (not all) of the homosexuals I have known claim that they have been homosexual since birth. Let's assume that this is true, that homosexuality is hard coded into some people's DNA, let's also assume that sexual intercourse with someone of the same sex is strictly prohibited by the Bible (which I am not sure that it is), I don't think it would be unfair or prejudicial to expect that a homosexual would refrain from sexual activity when they decide to follow Jesus, after all, self-denial is one of the primary virtues of Christianity. Christianity demands (among other things) radical self-denial, especially when it comes to the well-being of other people. For me, there are many areas that I would rather have the liberty to do what I want, as often as I want, but I don't because of the shared moral code of my Christian community. Even though I feel like I am hard-wired in a way that makes it very difficult to practice self-denial, I am still expected to practice the same morality.
I'm not sure how clear that was, but it was the best I can muster. So, to answer Emery's question, I don't think there is any good reason to prohibit same sex marriage (as long as it was open for all same sex couples, not just those who are homosexual), though there may be good reasons for some Christian communities to ask that the homosexuals in their midst practice celibacy.