At one point I started developing a religious RPG character who applied theoretical computer science to his faith.

I forget details, but among other details he believed that although the Bible prescribed the best way to live, the world is far too complex for any finite set of written rules to cover every situation. The same limitation applies to human reason: cognitive science and computational complexity theory have shown all the ways in which we are bounded reasoners, and can only ever hope to comprehend a small part of the whole world. Reason works best when it can be applied to constrained problems where clear objective answer can be found, but it easily fails once the number of variables grows.

Thus, because science has shown that both the written word of the Bible and human reason are fallible and easily lead us astray (though the word of the Bible is less likely to do so), the rational course of action for one who believes in science is to pray to God for guidance and trust the Holy Spirit to lead us to the right choices.