Whether or not aikido is in contradiction to your Christianity depends on the dojo (there are all kinds) and on your particular style or "brand" of Christianity. For the most part, I think aikido in the US is fairly non religious in it's applications, even with regards to O Sensei's own religion since most of his students said they didn't understand it either! I am a Christian and a pastor and I have not encountered anything that affected my being a Christian but if I ever did, I just wouldn't participate in that particular thing. Always be true to your own conscience and don't ever do anything that violates that for anyone else-they won't have to answer to God for what you do-You will.
God bless and enjoy the journey!