Honestly, you are probably the only person who she has ever known to outwardly label themselves an atheist. Discover the joys of a non-sexual relationship and find sincere ways to show affection without sex. When those are not around or when the circumstances or the spirit indicate otherwise then prayer is more than enough. I would go ahead and make boundaries with the conversation about kids and church, if that is your preference. I am a lawyer married to a surgical oncologist. I married a non-member over 20 years ago. It would be ludicrous to think otherwise. Many others have asked the same question in the past so you may want to find those and read the responses there. But remember that it is also your wife's choice to obey or disobey, and that you have no authority over her as a person, either. Controlling Behavior in Relationships.
I am a non Mormon. I married a recent convert girl в she may as well have been a nonmember в and less than a year later we got an annulment. This insecurity is at the root of the princess syndrome. I look back the 13 years with such sadness and loneliness; I was extremely busy and had no time for myself or others. We have almost daily prayers, scripture reading, and lengthy discussions about our beliefs. It did not go well.
Mormon children are advised, in their religion, to refrain from dating until they are at least 16 years of age. I believe rules are to be obeyed. Only idiots are unfriendly to non-Mormon spouses. He also travels an inordinate amount.