I don't really have a lot of answers, but I am interested in this as well, specifically the Balkan Wars you mentioned. I always found it troubling to see the Serbs, Romanians, and Bulgarians fighting, but I guess our Western counterparts fought many bloody wars as well. I know there is a lot written down about relations between the Russian and Georgian Churches during the most recent war, but like you said, this is highly politicized, and some of the dialogue between the Churches seems to have been politicized as well.
I remember hearing a story that this question was asked by Japanese Orthodox Christians during the Russo-Japanese War, and they were instructed to pray for their country. I don't know if this is apocryphal or not, perhaps someone has a source for this?
Perhaps you could throw in some insights as to the opinions of Orthodox Poles concerning the numerous wars that were fought between Russia and Poland throughout the years?
I find it troubling not just that Orthodox may have fought against fellow Orthodox but that wherever brother fights brother it reflects the fallen nature of man. Abraham Lincoln said it best during the American Civil War following the Union defeat at the Second Battle of Bull Run in August, 1862:
"The will of God prevails. In great contests each party claims to act in accordance with the will of God. Both may be, and one must be wrong. God can not be for, and against the same thing at the same time. In the present civil war it is quite possible that God's purpose is something different from the purpose of either party---and yet the human instrumentalities, working just as they do, are of the best adaptation to effect His purpose. I am almost ready to say this is probably true---that God wills this contest, and wills that it shall not end yet. By his mere quiet power, on the minds of the now contestants, He could have either saved or destroyed the Union without a human contest. Yet the contest began. And having begun He could give the final victory to either side any day. Yet the contest proceeds"