Re: Thinking of taking aikido!
there is no difference between praying and meditating. i know many christians who have practiced zen and said that it assists them in prayer. my zen teacher was from catholic poland and told me that he frequently prayed/meditated together with christian munks. our zen group's accountant is a devout christian and even took a half year reclusion in a greek nunnery after a year of zen practice.
that aside, the spiritual aspects of aikido are more practical than anything else and have no conflict with cristianity, islam, buddhism or other faiths in terms of doctrine.
good luck to you finding a nice dojo