I have to say that whoever told you that you should not practice Aikido due to your Christian beliefs was definitely misinformed. I grew up in a very religious household, the son of an Episcopal priest, and though I don't actively practice Christianity anymore I can assure you that Christianity and Aikido are in no way contradictory. Christianity at its heart teaches unconditional love. Aikido teaches us to love and respect even those who maybe trying to hurt us. Though I'm really just a beginner in Aikido, it seems to me that Aikido techniques don't truly become refined until the Aikidoist can do them with love, which comes with time (sure, you have to be doing the techniques correctly as well). In Ki Society, we read "Ki Sayings" at the beginning of each class, some of which have spiritual connotations that do not fall under traditional Christian dogma, but our Sensei's always tell us that it is not necessary to buy into the religious aspect of what is being said, because there are always other, more important points being made such as keeping a calm, immovable mind or the concept of doing good deeds without hope of a reward. Rachel made a good point that Aikido is a martial art, not a religion. If you are interested in Aikido, I really recommend taking a class or at least going to a dojo and watching a class. I promise you the experience will not turn you into a heathen!
Good luck to you.