RS,
I want to tell you that I too have those thoughts. We are from the good side because we always will think of the innocents who are killed. I think that it is good to regret the lives lost. We should not harden our hearts to feeling human, as it is a human trait which allows us to empathize with others.
What a person needs to do is allow his mind more influence over his feelings. It is a difficult thing to do but I believe that Judaism provides us a method to use both our head, and our heart, in our service to Hashem. Because we are composite beings, composed of a spiritual soul and a animal soul, we must be able to deal with conflict and opposition. I always see it as a balance between the trait of Chesed, and the trait of Gevurah... In english this means the conflict between the trait of kindness and the trait of strength or restraint. We all strive to be kind, but there are times we must hold back kindness, and even deal with strength... This idea is demonstrated in the story of the Akeidah, the binding of Yitzak on the altar by Abraham. Abraham was a man of unimaginable kindness, his hospitality is legendary, and yet Hashem asked him to sacrifice his beloved 37 year old son and this required him to act in a way which most don't consider kind.
And Ecclesiastes contains the phrase "A time for peace, and a time for war"... We must be prepared for both eventualities...