Given his Biblical knowledge it's by far more likely that he simply knows the relevant Bible passages.

He isn't a supernatural believer, though. It's only logical to close your eyes when they're opening it; either it disintegrates everyone but you (because your eyes are closed) or nothing happens, in which case it makes no difference that your eyes were closed. It's exactly what any sane, rational human being would do when presented with a device that they don't understand but have received some instruction (however much you believe it) regarding how to handle it.