Shane, I, too, am a Christian who just started aikido. I did a lot of reading on the topic, and decided that as long as your motives are correct (self defense, not offense, ie) and watch your step around aiki issues (nature and purpose of man, among others), you'll be fine.
Don, not sure, but maybe because "Ai Ki Do" is actually three words, and is usually translated with caps: "The Way of Universal Harmony" (one translation) and not "the way of universal harmony"...they mean the same thing, but the first is a name, the second is not.
(BTW, not putting all that there for your sake, I'm sure you know what aikido means and such...just making myself clear for others)
Opher, why don't you enlighten us? lol
Shane, hope you have fun!