First off, let me say that I think the civility with which this thread has proceeded is a credit to the open minds of this little aikido community. When I saw the opening post I too thought it was quite 'dangerous'.
I am not a Christian, though I was brought up as one. It was about that same age (~13-14) I started questioning things and found my own path. I look at christianity like any other religion: as a collection of stories, mythologies, beliefs, and practices interrelated with specific cultures and customs.
It is easy to look at the literal / institutional side of chistianity and its (continuing) history of violence and intolerance and form a very negative view of it. The one thing i cannot tolerate is intolerance.
However even as an atheist i recognize the importance of spirituality and cultural practices to the individual and society. I even know 'non-believers' who attend church regularly. I see no harm in the practice of gathering and talking about being nice to each other once a week. For the record I was a practicing Soto Zen Buddhist for a while, which for me was a secular practice of disciplines like sitting meditation, with deep cultural (religous) roots which enhance the feeling of participation and the ultimate value of the experience.
That being said I think there are features of christianity in particular which foster intolerance. I'm no religious scholar, but I would guess this developed as a result of the church becoming a major (and ruthless) socio-political organization in europe. Of course, most christians I know despise this aspect as much as I do, but it is alive and well here in the U.S.. Sen. Leiberman, the DEMOCRATIC V.P. candidate of all things, said "The Constitution guarantees freedom OF religion, not freedom FROM religion". Egads.
Back to the Aikido relationship: I also see no conflict. I know very little about Omotokyo, O-Sensei's major spiritual influence, but I think it offers a broad interpretation which recognizes the spiritual aspects of all things, flowing from some original, all-encompassing source, which can ultimately be compatible with just about any religion. Or I could be way off-base about that. All I know about it I read on the FAQ and whatnot.
-e preston (Zow, sorry about the length)