The stars must be aligned, because on the very day that I reposted my Parable of the Three Jews, my friend Wolf posted on the new BAR article, a four-part interview with four professors (including Modern Orthodoxy's own Lawrence Shiffman) about how their scholarship has affected their faith.
As I might have predicted the two professors who came from literalistic/fundamentalist traditions are no longer believers. For them it was all or nothing. But the two professors who ascribed to more flexible religions (including Modern Orthdoxy's own Lawrence Shiffman) report that facts and faith can coexist. As you learn more, you may end up believing in less, but the essential parts of Judaism can't be disproven by the facts of science and history; belief in those essentials can remain forever intact if you haven't been taught its "all or nothing."
This, incidentaly, happens to be my own experience. Even as I discover more and more about the world and the past, my faith in the essentials remains unshaken.
More:Aside from Wolf (see above) XGH, Hirhurim and Fred have weighed in so far...