One of the things that is hard to grasp about In Nomine is the uncertainty of certain religious concepts. Angels do not know if Jesus was really the son of God, if Mohammed was the new direction of the worship intended by God, if the Pope is really infallible. How is this possible?
Well, the first being killed in Lucifer’s rebellion was the Metatron, the voice of God. After that point, God could no longer speak directly from the Higher Heavens to angels. Yves had always been good at interpreting God’s will and continued to do so, though not everyone trusts him, notable Michael, Archangel of War.
While there have been actions by God since that point, the inspiration of Mohammed, the summoning of Uriel to the higher heavens, the giving of Words, God has not spoken to the heavenly host and thus there is room for disagreement that has festered into politics.