I would recommend the following steps:
1) Find her objections 2) Assure her that you understand that her objections feel valid
You can, if you like, try to explain why her objections don't feel valid to you (unless of course, they do) but try to keep the conversation away from facts, premises, or rationality. The odds are very high that she is not becoming hysterical about you becoming an atheist because of some rational process. The odds are also very high that she cares more about feeling listened to than about your atheism. Try to steer clear from why you are an atheist: don't invite an argument where there doesn't have to be one. It likely won't be a productive argument if you have it. Definitely steer clear of directly attacking Catholicism: the odds are high that she has heard such attacks before and it could cause a negative social grouping that it doesn't sound like you want.
I'll leave you with one thing that can help if you become frustrated with her that I learned from sales training: objections=interest. It can feel like your mom doesn't value your welfare or well-being, especially if you believe religion was doing bad things for you. But if she genuinely didn't value your well-being, she would be unlikely to bring up an objection to your atheism. She might be mistaken about what is good for you, but she's likely very scared and doesn't know how to handle this. Anything she says that is hurtful is probably best attributed to that fear.
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.