I'm also an atheist. When my wife and I got married, we did so in a civil setting rather than under the eyes of God in a church. Our choice.
While I'm an atheist, I also wholeheartedly respect the religious choices of others. If you want to believe in whatever your chosen deity wants you to believe, have at it. Live your life the way the scriptures of your particular religion tell you to. Shout your religion from the rooftops if you wish, and I'll respect your right to do so.
The minute you get a publicly funded career that allows you to directly influence the laws of the land however, park your religion on the lawn outside if you would be so kind. You're not in Parliament to follow your own personal crusades, you're there to represent (as best you can) the views of all the people in your constituency.
Sadly, this concept seems beyond the grasp of a number of Conservative MPs when it comes to the debate over gay marriage. What also seems beyond them is having the courage of their convictions to come out and say what they actually think.
If you believe it is wrong for people to be able to marry someone of the same gender, if you think it is somehow an affront to your god and to morality, at least have the balls to come out and say so. Take your position and stand by it. I'll regard you as a bigot not fit for public office, but I'll have at least a grudging respect for your forthright defence of your viewpoint.
Just whatever you do, please don't come up with some weasel excuse about it "not being a priority", or that the government has "other things it needs to be doing". You're fooling nobody with that one. If you're against it, just come out (if you'll pardon the pun) and say so. When it goes to a vote, which side of the fence you came down on will be a matter of public record so your stance on the matter will be out there for all to see.
It's not beyond the remit of even the most inept of governments - and this one is pretty close to the top of the charts in that category - to deal with both social and economic issues simultaneously. More than one piece of legislation is moving through the houses all the time. It has to be, otherwise nothing would get done.
If your MP is one of those who is trying to delay the vote (until such a time as they are out of office and won't get their bigotry exposed, presumably) and believe that everyone should have the same rights to be married irrespective of their sexuality, I hope you bear their actions in mind should they come up for re-election. Parliament is no place for racists or sexists, neither should it be for homophobes.