Johannes,
From my own experience, I would guess that it isn't so much aikido that is in conflict with Christianity, it's the fact that you are _15_, and looking around you and seeing how much is wrong with "Christendom" and "Christians", rather than Xianity itself.
Read Kierkegaard
In other words, you would be doing this soul-searching even if you had never heard of aikido.
Things will never be the same, but they can get better.
=wl