I am also a catholic aikidoka. In our dojo, when we rei toward the shomen, we are giving thanks to O'sensei and to anyone who has ever taught us anything of value. I don't worship my sensei when I rei to him, but I am often thanking him.
I see ki as simply another way of explaining physics to other aikidoka. If they extend their ki and it has the desired result of making their technique better, what's the difference?
As for the martial aspect, the catechism explains the right - and the duty - to defend yourself in pretty good detail.
Many times over I've thanked God for helping me find aikido. It changed my life for the better and I think it's something that I can teach others to help better their lives.
Sad, frustrated, imbalanced kid + aikido = pretty nice guy (at least in my case).