There are those in this world that will be intolerant of anyone not doing things that fit into THIER worldview. I am not currently studying Aikido but my Kenpo instructor studied Aikido before joining the U.S. Army (he's one of those Airborne Ranger types).
People have told me that MA's don't fit in with the "Christian" ethic of "turn the other cheek". We as martial artists know that the goal of martial arts is to AVOID conflict. I believe the ethics of Aikido go hand in hand with Christianity. But anyone who has read the "Tao Teh Ching" and the "New Testament" may think that Taoism and Christianity aren't that far apart.
So if people tell you that you are damned for studying a MA, then smile and realize that you know the truth of it. A warning note tho, anything in your life can become a detractor from your faith no matter your religion. So best of luck to everyone.
what you do,
when it counts.