I agree with Kkun and Yukuo - the 'Christian Saga' misrepresented Christianity rather than purposely tried to bash it due to ignorance. You have to realize that the Japanese are mostly into Shintoism and Buddhism and they don't really understand Christianity. So anime series usually blow it when they try to depict Christians.
The whole feng Shui story arc was pathetic filler episodes. Believe me, you weren't missing anything when CN decided not to air those stinkers.