One of the most difficult things to do is argue against the historical "urban legend" type of arguments that agnostics throw in the face of Christians. It is difficult because it must be done again and again with little apparent effect. For instance, the theologians of the Medieval world never taught that the Earth was flat. Aquinas, for instance, knew it was round. Yet again and again you will hear people say that Medievals were afraid of sailing too far from shore since they thought they would fall over the edge.
One recurring myth concerns the figure of Giordano Bruno, a putative scientist who died defending Galileo's ideas. In fact, Bruno was apparently an unlikeable man in a number of ways, and he got himself into trouble for practicing the occult and for being nasty to his sponsors. Today, we would insist that it was wrong to burn him for his views, but we would be right to say that he is not a poster boy for Reason and Enlightenment.
The problem is, of course, that even with these kinds of refutations, such historical myths seem to live on. This suggests that those who accuse Christians of being fearful of using their intellects are in fact afraid themselves to alter their own erroneous views based on reasonable evidence. The opponents of Christianity often base their arguments on subrational desires to be free from religious constraints, not on real historical truth.