What do I do? I don't know how to react/behave when she's doing this.
Walk away. Definitely don't engage or react emotionally, that just rewards the codependency.
The other option it may be too late for: Lie. When in Rome do as Roman (Catholics) do. Sharing details about your models of reality is something you do for your own benefit with people who can interact with it in a way you consider useful. It's not something you are obliged to do with people who are unstable, controlling and ineffectually manipulative.
Yesterday my mom noticed (at a funeral) that I wasn't praying or participating in the mass. She confronted me about it, and I told her that no, I am not Catholic. Apparently it's sinking in and she's a bit hysterical... crying and screaming that she doesn't know me anymore.
What do I do? I don't know how to react/behave when she's doing this. It's like she wants me to feel like I'm doing something wrong, but it isn't working, so she's getting hysterical.
*edit*
I gave her a hug when she calmed down and told her I love her. That seemed to help, a little. Based on her previous behavior in situations where I've done something "wrong," she will (in the future) make barbs and slight passes at my beliefs. (Already she made one: insisting my love of science is causing my social anxiety disorder.) The advice given in the comments is really helpful. I plan on making the most of it.