My mom sounds a lot like your mom. She was raised by her grandmother though in a Pentecostal church in Virginia and believes that is why she is the person she is now. We had a long talk a few months back because I have become more vocal about my beliefs. It bothered her that she thought I was criticizing her grandmother (who she loved as a mother) for how she raised her.
I explained to my mom that her grandmother raised her well in spite of what the Old Testament taught her. My mother is sweet, caring, generous, and hard working. I had to tell my mom that the Old Testament does not promote most of these qualities, and nor does it exemplify any kind of moral code that people should live by EVER. Luckily, my mom is pretty open-minded and was willing to hear me out. I don't know if she agreed with me at any point, but she was willing to listen and ask questions.
In the end, we came to a peaceful understanding. I made it clear that I am no different than I ever was, and asked her flat-out if she thought I was now a bad person, to which she answered 'no'. But I also had to agree to try not to convert her or "laugh" at her religion, and she did the same for me. Her decision to allow me my atheism contradicts her religion's beliefs. Yet, she was willing to compromise with me. I think that's a great sign. :)