I think many Libertarians have been hoodwinked on the marriage issue. There are several views which popular Libertarians seem to take. One is "the government should not have anything to do with marriage". Another is "the government has no authority to not allow gay marriage".
The problem with both of these opinions is that they are naive about the fundamental integration of marriage with society. In other words, marriage and children are such a fundamental part of society, that if a government ignores these institutions, the government has, in fact, ignored the society it is supposed to govern.
It would be like setting down rules for basketball, but not mentioning the basket or the ball.
The fact is that marriage and its expectations - for society, government, contracting, obligations, responsibilities, presumptions, etc., require that governments have some working definition of what marriage is in order to deal with it effectively. Is a child being neglected by his parents? How could you who his parents are without a marriage policy? What about custody rights in divorce cases? Again, some view of marriage has to be presupposed. It *cannot* be contract law, because the responsibility and upbringing of a human being is outside the realm of contracts. Husbands and wives don't have to testify against each other. Again, this presupposes some view of marriage.
Now, Libertarians don't want the government involved with the marriage process. I agree with this totally. However, this does not mean that the government shouldn't have a definition or understanding of marriage. The best Libertarian option is not to leave marriage undefined in governance (and, by extension, to have governance have no relevance to human life experience), but rather to re-establish common law marriages.
Common law marriages are marriages which the state recognizes without the participants having to have gotten an official state certificate. The nice thing about having a certificate of marriage is that the state makes its position on your relationship official and clear. The nice thing about common law marriages is that it allows you to live your life free and clear of the state so long as you are living within proper bounds. It is only if one neglects their duties that the state becomes involved at all.
To put it succinctly, I think the Libertarian idea of leaving the concept of marriage out of government is foolish and naive, and this latest wave of naievity has caused many normally clear-headed Libertarians to essentially sit out the marriage policy debate, for the worse for us all. The better option is not to ignore or sidestep marriage policy debate, but rather to find ways, such as common law marriage, in which people who are living rightly can pursue their lives completely unencumbered by the state.