Gambatte,
There is ABSOLUTELY NO religious conflict between meditation and religion. Clearing your mind and relaxing your body is not praying to some Shinto god. I believe many Christians even use it. As for it being wasted time, this is absolutely incorrect. Meditation is training. By relaxing and pushing the day's thoughts out of your mind, you become much more able to focus on your physical training. Not to mention that it has always been used in many Eastern martial arts, especially the Japanese, because it helps prepare your mind for violence, both to face it and to commit it. I'd recommend taking a new look at meditation. There are certainly ways to use meditation for religion, and it finds its way there, you're correct, but it does not have to be, especially something like Zen meditation which is so useful to martial arts.
Bladesaint,
I completely agree with you about Chi Gong and Tai Chi as meditation. When I practice my kata, I will sometimes attempt a "moving meditation," in which I attempt to completely empty my mind and allow muscle memory to operate while I'm performing kata. I believe it's functionally similar. Most of the time, though, I train kata more for the physical motions.