Why does Margaret Jean allow John to take the baby from the church in the book, Lucky: A Novel?

Margaret Jean is a nun at the church where Valerie left Lucky. She is on the run from something when she uses fake records to earn a position in the church, and she is upset that she is going to have to take action the night Valerie leaves her baby at the church. As a result, she allows John to take the baby because it eliminates her need to do anything.