Interestingly enough, it's not been "too long" since tacticians drew upon supernatural support. Ian Fleming once reported that in World War II, not only were the British using pendulum reading to divine Axis intentions, but the Nazis were too and were actually having more luck with it.

Hitler and many of his cabinet members were actually major followers of the occult, which was very popular in the Roaring Twenties in Europe. As a matter of fact, the whole Nazi régime can be described as a "faith-based" program, since the Nazi conception of Aryan destiny was, to a large extent, derived from the Theosophical writings of Madame Blavatsky. Not to mention the close ties between the Nazi Party and the Thule Society, or the Schutzstaffel's initiation mysteries.

Therefore, I wouldn't be particularly surprised at all if Dubya did indeed institute a faith-based missile defense system. These types tend to be drawn to such schemes.