How would you handle these conflicting messages with your kids?

My son’s oldest daughter spends Sun morning – Wed evenings with her Mom, who suddenly became a Christian somewhere down the line, and Wed. evenings to Sunday mornings with her dad, my son, who quietly became an atheist somewhere along the line. (I raised them in the Christian church. Seems like we spent half our lives in church! I also kept my change of heart under wraps for them as well.)
His daughter has been asking why they don’t have Jesus on the Cross in the middle of their dining table? Why don’t they pray? And on and on.
My son is handling it very well, and very respectfully, and leaving her room to make up her own mind. She’s very analytical so you can guess where that’s gonna lead!
He doesn’t tell her her mom is wrong, says nothing negative about religion he just says he doesn’t believe that. He also asks her questions designed to make her think. They have some pretty interesting discussions about it I guess.
I don’t expect as much from her mother, though. I can imagine her getting very strident about it.