I think they should be allowed to, I see no reason why not, and I totally understand why they would want to if they are religious.
However, I believe it should be entirely the choice of the church to decide its own matters, as long as they do not actively harm anyone, or effect people outside of their religion with their actions then they should be allowed to make their own rules.
I think its very hypocritical of the a lot of the atheist public to criticise the affect religion has upon their lives and then push their views upon the rules of the church.
I don't want the church interfering with the government politics (even thought of course they do) and so I see no reason why the government should have the right to determine the policies of the church, so whilst I think its ridiculous and ancient to refuse gay marriage I also accept that its nothing to do with me and its for the leading bodies and the members of the religion, and the religion alone, to decide.