I'm not really sure what she says to him when she brings it up, but I know he tells her (More firmly and a little more harshly than I do) to mind her own business. And I know she brings it up when he says "Baby, where are the heathens? It's time for another amoral math lesson!"
I think she really IS concerned about their spiritual selves, their souls, what have you, but I also think she thinks I'm a terrible parent because of other things not just this. Like my kids are in preK and Kindergarten and they have chores. Well she thinks they are too young. My best friend is gay and she thinks allowing him around my kids is going to get them molested, killed, or damned to hell. Things like that.
I KNOW that she loves my daughters and I've told her that if she wants to or needs to pray for them, by all means, go ahead, that doesn't bother me at all. But I NEVER say a word when she makes a decision with her children that I wouldn't make because I find it disrespectful and rude. I just expect the same common courtesy in return.