It seems, at least, that she understands where the separation of views really occurs:
Based on my in-person arguments to date, it seems like most of my atheist friends disagree two or three steps back from my deciding Morality is actually God. They usually diverge back around the bit where I assert morality, like math, is objective and independent of humans.
As far as Catholicism specifically, she might benefit from reading Elaine Pagels, who discusses at length the historical evidence of the founding of the Catholic Church. Notably, the selection of gospels to include in the New Testament was made specifically to support and cement the authority of the church, not for any well-founded empirical or philosophical reasons.
Catholicism is an organization as well as a belief system, and the organization is terribly, systemically corrupt. An official conversion implies endorsement of the organization as well as the belief system. For a prominent (former) atheist blogger, this seems like a morally questionable act.
To the best of my knowledge, this is a misleading account of how the books of the Bible were selected. My understanding is that it was as much of a popularity contest as anything.
And while you can identify a "proto-orthodox" faction among the various Christian groups fighting as early as the 2nd century, it was very different than today's Catholic church, or even the Catholic church of Aquinas' day.
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!