Hate to be self-promoting, but I just wrote a blog post on this that you might find useful.
Given that conversions tend to be driven by people's personal connections, probably realistically the best thing you can do to stop something like this (at least in the future) is get someone a good support network of non-believing friends.
Though that's probably not what I'd do in your situation. I'd be screaming at hear that the Catholic church is evil and if she must be religious, why can't she be a nice Episcopalian or something? Which is kinda what I do in my blog post, who knows if she'll follow the blog ping to it.
Um, as a slightly nicer approach that will still get at the "Catholic church is evil" thing, you might try to get her to read William Lobdell's book "Losing My Religion," which talks about how (among other things) being a journalist covering the Catholic sexual abuse scandals led to him leaving the church.
I recently learned that a friend of mine, and a long-time atheist (and atheist blogger), is planning to convert to Catholicism. It seems the impetus for her conversion was increasing frustration that she had no good naturalistic account for objective morality in the form of virtue ethics; that upon reflection, she decided she felt like morality "loved" her; that this feeling implied God; and that she had sufficient "if God, then Catholicism" priors to point toward Catholicism, even though she's bisexual (!) and purports to still feel uncertain about the Church's views on sexuality. (Side note: all of this information is material she's blogged about herself, so it's not as if I'm sharing personal details she would prefer to be kept private.)
First, I want to state the rationality lesson I learned from this episode: atheists who spend a great deal of their time analyzing and even critiquing the views of a particular religion are at-risk atheists. Eliezer's spoken about this sort of issue before ("Someone who spends all day thinking about whether the Trinity does or does not exist, rather than Allah or Thor or the Flying Spaghetti Monster, is more than halfway to Christianity."), but I guess it took a personal experience to really drive the point home. When I first read my friend's post, I had a major "I notice that I am confused" moment, because it just seemed so implausible that someone who understood actual atheist arguments (as opposed to dead little sister Hollywood Atheism) could convert to religion, and Catholicism of all things. I seriously considered (and investigated) the possibility that her post was some kind of prank or experiment or otherwise not sincere, or that her account had been hijacked by a very good impersonator (both of these seem quite unlikely at this point).
But then I remembered how I had been frustrated in the past by her tolerance for what seemed like rank religious bigotry and how often I thought she was taking seriously theological positions that seemed about as likely as the 9/11 attacks being genuinely inspired and ordained by Allah. I remembered how I thought she had a confused conception of meta-ethics and that she often seemed skeptical of reductionism, which in retrospect should have been a major red flag for purported atheists. So yeah, spending all your time arguing about Catholic doctrine really is a warning sign, no matter how strongly you seem to champion the "atheist" side of the debate. Seriously.
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. Of course, I would prefer most that she stop worrying about religion entirely and just grok the math that makes religious hypotheses so unlikely as to not be worth your time. But in the short term I'd settle for her not becoming a Catholic, and not immersing herself further in Dark Side Epistemology or surrounding herself with people trying to convince her that she needs to "repent" of her sexuality.
I think I have a pretty good understanding of the theoretical concepts at stake here, but I'm not sure where to start or what style of argument is likely to have the best effect at this point. My tentative plan is to express my concern, try to get more information about what she's thinking, and get a dialogue going (I expect she'll be open to this), but I wanted to see if you all had more specific suggestions, especially if you've been through similar experiences yourself. Thanks!