Not to second guess the lyricist, but it would have been just as easy to write a lyric about a pair of drug-abusing parents who went to church each Sunday and when the girl got to her new family, she got to express that she was always glad about Jesus, despite the fact that the rest of her life was terrible, or maybe that she was scared about losing Jesus along with her bad parents, or something like that. At some point, there was a specific choice to make the bad parents not be churchgoers. Whether that was for the payoff or because of some prejudice against atheists I cannot judge, nor can anyone. But appearance means a lot. What if, instead of atheists, the bad parents had been identified as black? Yup, that poor girl with her crack-smoking black parents.