Once you have some understanding of Aikido etiquette as to what is spiritual and what is just a show of respect (bowing, etc.) there shouldn't be a conflict with most faiths that I'm aware of.
Nick, the thinking expressed in the "if we don't know what it is, it must be from Satan" is just plain dumb. Kind of ironic, but today at church in the gospel reading Jesus is passing through a crowd, and a woman who wants to be healed presses forward and touches his cloak and is healed. The scripture says something to the effect that he turned because he felt "the energy go out" from his body.
Don't know if that's "ki" but it sure ain't satanic!