I can't believe I am partaking in thread necromancy (6 years old)...but here goes:
This subject has/is also of interest for me, but for entirely different reasons. I come from the perspective of someone who spent several years in the seminary preparing for the Roman Catholic priesthood. In the end, I chose not to pursue that path as it ultimately was not a suitable lifestyle for me (i.e. that whole celibacy thing...I admit that I enjoy the company of women too much
). Regardless, I received an excellent theological education. I still am a practicing Christian, BTW (a lot of folks incorrectly assume that if you drop out of the seminary, you're automatically a "fallen away" Catholic or that you somehow lost your faith).
My take on the issue is that we first must differentiate between Catholics, Protestants and Evangelicals when we discuss this issue. Just as with Buddhism (or any other religion), Christianity has several diverse denominations, sects and factions that sometimes dramatically disagree with each other.
From my experience, Catholics (even devout ones such as myself) usually don't have a problem with Aikido...even with it's most traditional and overtly Shinto aspects. Why? I think it is because Catholicism is very symbolical in its essence: sacraments, liturgy, saints, hierarchical clergy, etc. I can easily find several parallels between Catholicism and Aikido...far too much and too detailed to write here. They all compliment one another quite well and Aikido has become a devotional for me, with bokken and jo as rosaries.
Protestants (by this I mean mainstream Protestantism such as Lutherans, Methodists, Presbyterians, Anglicans, etc.) by and large don't have too many problems with Aikido, either. Many of the mainline denominations are very heavy into ecumenism and interfaith dialogue, so Aikido fits in quite nicely to that paradigm. However, it is a bit more nebulous though in that the more conservative the particular denomination, the more problems they have with Aikido.
The group of Christians that by and large have the most difficulty with Aikido are Evangelicals. Because they take a rather literal interpretation of the Bible as well as their aversion to any form of ritual (this historically stems from their distaste for Catholicism), Evangelicals regard Aikido as an "eastern religion." Bowing is considered an idolatrous act, as is the presence of the shomen...which is regarded as a pagan shrine of false gods (Shinto kami) and a false messiah (O'Sensei). Even more, that Aikido espouses specific moral principles as well as a distinct spirituality that encourages introspection as illuminated by O'Sensei, Evangelicals regard all this as constituting a religion. Of course, the fact that much of what is the body of "Aikido spirituality" is remarkably similar and quite complimentary to Christianity is often lost on Evangelicals. Oh well....