What do you do? I can't decide what is right for you in such a case, but I will offer some thoughts on the matter for you to consider.
I'll start by saying that I think the situation I have described, difficult as it is, tends to be far easier than a similar scenario involving one's family. After all, most people will have many more intimate partners during the course of their lives than they will have families. I realize this is not a pleasant notion because you'd prefer to maintain this relationship.
The central question I would want to ask myself in such a predicament is as follows:
How important is it that my partner loves me for being me rather than for being something he or she wants me to be that I am not?If I do not believe in gods, I would not want to pretend that I did. I would have a hard time remaining in a relationship with someone around whom I did not feel like I could be myself. I would want to give my partner an opportunity to know the real me. This might include my thoughts on the subject of gods and the manner in which belief in them affects the culture in which I reside.
It is fairly common for people in a relationship to be as attracted to the potential of someone rather than to the actual person. And yet, it has been my experience that such relationships are often doomed if they do not quickly progress beyond this point. If I am in love with what I want someone to be rather than what they really are, I'm resigning myself to being perpetually disappointed and unhappy. One could reasonably argue that this wouldn't be a relationship at all but merely a form of narcissism. In any case, it is difficult to imagine such a relationship working in the long run.
Of course, one may decide that maintaining this particular relationship is worthwhile, even if it means concealing one's true self. This wouldn't be my choice, but it is not my place to fault you if it is yours. Being an atheist can be lonely, and there is little point in denying that.