I was also raised in a roman catholic family, and attended a catholic school. My mother's sister is a nun. I know some people who care a lot about their religion and refuse to practice martial arts because they feel that bowing, and ki, and all this metaphysical stuff goes against their faith. It's because they do not understand. The bowing problem is another subject, so let's talk ki. I personally believe that science hasn't yet discovered - and may never will discover - all the secrets of the human creature. What I know for sure is that everything we are capable of, either physically or mentally, was given to us by God. I's still not sure what ki is exactly, but it does no bother me, and it does not interfere with my prayers.
That's my opinion. No, tha'ts my faith.