If it matters, I'm not a religious person. I think that religion generally causes more harm than good in the modern world, and certainly has no place in politics. But Harris' arguments about the role of the Church
before the modern era tend to be naive and uninformed.
What you say about Catholicism being "the only game in town" is really accurate, but you can't assume that a world without Christianity would have been somehow more intellectual. I don't really know what the Catholic church
did suppress during the Middle Ages, given how interested many churchmen were in accumulating knowledge and studying the natural world.
As for suppression, the Catholic Church throughout the Middle Ages had little interest in suppressing any ideology that was not explicitly theological. There is the obvious example of Galileo, but this was post-medieval, and much more complicated than "
science = bad". I am not aware of a single intellectual being limited for a non-theological reason, mostly because the Church was the only entity with enough resources to support the training and patronage of scholars. This hegemony is certainly unethical, but you can't suggest that there would have been just as much intellectual development otherwise. And you
certainly can't claim that we would be "more advanced" today, as people like Sam Harris and yourself often do.
If, somehow, the Catholic Church was abolished in 1100, who would be able to promote intellectualism? You need to realize that there were no philosophical academies in the post-Roman era, and that all universities were somewhat ecclesiastical. Lay rulers didn't really have much interest in promoting intellectualism, and those that did (such as Charlemagne) were often mostly concerned with recording their own history and educating their children for political gain. Your suggestion that the Catholic church actually hampered the Whiggish idea of progress is unfounded and intellectually dishonest. Sam Harris' fervent conviction to that misconception is why I believe that Dan Carlin shouldn't have organized this dialogue.