Most churches, including the mainstream ones that pride themselves on historicity, aren't pacifists.

There are obviously some protestant churches that are pacifists. However, Catholics and Orthodox are not outright pacifists. The Catholics have had a number of pacifistic groups within, the most notably the "Catholic Worker Movement" of which Dorothy Day was a part. Pacifism is not unheard of in the Catholic Church. The prevalence of non-pacifism in the Catholic church should not be surprising, however. The Catholic church (and the protestant churches which came out of it) have always been much more juridical and legal in their approach to theology. This line of the church has long found itself married to the state. In fact, the church and state eventually became inseparable, and such a theology lead to many of the horrors with which we're familiar in the Middle Ages. The living out of a church-state theology have lead to atrocities we still can't escape from today, when atheists bring up accusations of how Christians don't really seem to be like Christ. 

In the Orthodox Church, however, their stand is much more pacifistic than you might think. By and large, the church views wars as necessary, but not justifiable. So if a soldier engages in a war and kills, while that action may have been necessary, the soldier is still required to repent. In fact, some Orthodox traditions say that one cannot be a religious worker if they have ever shed another's blood - even if that blood was shed by accident. I found these ideas confirmed by many sources, but this source is perhaps the best overall synopsis which also provides external links. If one is not a pacifist, I find the Orthodox tradition to be much more in line with what was taught in the early church and by Christ than most protestant denominations.