No specific advice, but I'll offer you my story which had some similarities in the beginning you yours.

I (male) was like you, non-religious and indifferent to religion, although I wouldn't have labelled myself as an atheist at that time. My fiance was a practicing Catholic from a devout Catholic family but didn't seem to mind my non-religiosity. Before the marriage, we discussed the issues and came to what I thought was an agreement. She was okay with me being non-Catholic and non-religious. The religion was important to her so I agreed to allow any children to be brought up Catholic. I also agreed to go to church with her "occassionally". She gave me a finger-wagging lecture about how I better be serious about the marriage, because, "I'm a Catholic and marriage is forever, bla, bla...". But it wasn't long after the wedding before my lack of religion started to irk her. She didn't like being a married woman going to church alone and was always pestering me go to church with her.

There were some other factors involved, but long story short - the good little Catholic girl ended up having an affair less than five years into the marriage, got pregnant by her lover boy, and had an abortion. I initiated a divorce and she got pregnant a second time before our divorce was finalized. After the divorce she applied to the RC church for an annulment (and got it) so she could get a do-over.

The process of dealing with the RC church in the wedding, the ongoing marriage, the divorce and the annulment opened my eyes to the insanity of religion, the hypocrisy of the church and of religious people, and planted the seed of the atheist and anti-religious sentiment I have today.

Actually, looking back, I am glad the marriage ended because I'd probably be up to my armpits in Catholic bullshit now. I just wish I had stopped the nonsense before it all got started.

I guess the only warning or advice I would make to you is that people's behavioural traits generally tend to intensify as they get older. Often the religious get more religious, the ambivalent non-religious turn into atheists, the quirky get more quirky. So any small cracks in your relationship will probably get bigger.