Closeted atheist in a tangled situation. Soliciting friendly opinions and advice :)

I looked around on the FAQ and searched for something similar to this, dreadfully sorry if it's some form of a repost.

Setting: I've grown up in a deeply conservative Christian family. Very active in my church as part a familial thing, serving in the weekly services, teaching kids in the youth group, and a whole host of other things. I've found an amazing woman who I'm currently engaged to, working towards our college degrees at a local university, we'll call her Lilah.

Quandry: As time has gone on, aspects of Christianity have begun ringing quite hollow to me. I'm well resolved to incongruous concepts and I'm comfortable letting them remained unresolved, but many of them are coming to a head, especially in the realization on the strictures of a life lived to the edicts of another. (i.e. humanity has much more potential, ethos, and morals if it is working towards betterment because it's right, not because we're told to)

My parents are fairly resolved that I have pretty different ideas then them and they tend to trust in my intelligence. They will not be resolved to me having any form of atheistic thoughts. I still live in their house although I own my own car and I'm putting myself through school. I'm very close to my family, and I'm fairly positive that if I walk this line, I'll be essentially excommunicated.

There is little to no doubt in my mind that Lilah would end our relationship. I've softened some of her more absurd, deeply conservative notions by love and logic, but I know that it hasn't gotten to point that she would be accepting of a new tract. I'm a very lonely individual who managed to find a incredibly healthy relationship that has been wildly beneficial to me in many areas, so the idea of destroying that is a little more then I can comfortably think about.

In the meantime, I've been trying to foster love and tolerance in my church's youth and in my family, not arguing from strictly Christian standpoints, but just from the knowledge that it's good. I want to spend my life with Lilah, but I know that if the only reason that I stay with a church is her, I'm going to develop a resentment towards her. Hurting her is the last thing I would ever like to do, but I'm feeling like my options are whittling away.

TFL;DR: My entire intimate connection to the human race is built around Christianity, which I'm rapidly losing respect for and belief in. Advice?

Edit One: Lilah and I have always had great communication in our relationship. I've talked to her about many similar topics and about general being disillusioned with religious things. This post is from some more recent developments in my beliefs on things; which I have not yet discussed with her. Thanks again :)