I think it largely depends on how adamant on or both of the spouses is about the religion issue.
For me, I am much more concerned that my children grow up to be patriotic and moral citizens that faithful churchgoers.
To me, the fact that someone goes to church means nothing. I see people who go to church every week screw people in business all during the week and yet hold themselves out to be good people.
I see many people who never set foot in a temple or church yet are the best people on earth.
I refuse to believe that God will accept the churhgoer who treats people like crap while ingoring the moral decent person who does not.
This reminds me of a funny story from my youth. A buddies dad was both the owner of the only local car dealership in the small midwestern town (Ford) and the head of deacons at the local church. My friend remarked "the elders decided that my dad had screwed so many people out of so much money all week that by the time Sunday came around he'd be too tired to steal more, so have him count it". It was said with a smile, and obviously he was well respected.
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I see many people who never set foot in a temple or church yet are the best people on earth.
I see people who are religiously very devout and who live lives of decency, kindness, and love.
I see people who don't believe in any religion who are alcoholics, adulterers, wife beaters, pedophiles and murderers. And those are the celebrities!
You argument that SOME people who don't belong to a church are "better" (a subjective judgment at best) than SOME people who do belong to a church, is irrelevant.