This could get dangerous. My general take is that there is no reason that Christianity and Aikido cannot coexist. Aikido is not a religion, although it gets treated as such by some, and should not be in direct conflict with the church. Now some church loonies might have issues with Aikido but that's a different matter and why I tend not to have much regard for the church itself.
I would also be careful of taking Seagal too seriously. I would no more look to him for spiritual guidance than I would ask the local celibate priest for advice on sexual practices. They both will be glad to give advice but what's it worth?
I used to practice Aikido with a father Avila. He was a very nice guy and didn't seem to see any conflict between Aikido and the church. Your Aikido instructor isn't Aikido and the church is not Christianity.