But second, and more immediately, I wonder if anybody has advice on how to handle this, or if they've had similar experiences with their friends. I do care about this person, and I was devastated to hear this news, so if there's something I can do to help her, I want to.

Why are you so convinced this is bad for her? Most people are somewhat religious, and every study I've seen suggests they are just as happy, well-adjusted, and moral as non-religious people. I certainly think it is generally better to believe what is true, but is something like this really worth being devastated about? Can't you just be open-minded about her lifestyle choice?