The ideas in this story were every bit as thought provoking as other commenters have said. And reading the comments has given me a greater appreciation of the story. Now I wonder if the Decharai were even aware that they were in a war. But I thought the story was too long, and the military characters too cliche (can we please have one high-level officer who knows what's going on? I know they are out there). The friendship of Christian and Muslim seemed a little forced and remarking on it in the far future was as illogical to me as remarking about my friendship with a Jew or a Japanese or a Black person. I also couldn't get past the lack of futuristic, or even modern, weapons. We have sites on our own planet that have been nuked and are now vibrant cities or ecosystems -- heck if the ozone layer was so thin the planet was being bathed in radiation anyway. There are also poison gas, robotic drones, bunker busters...
But again, the idea of aliens that effortlessly dish out enlightenment and that necessitates humans killing them is well worth the price of admission. A better fit on Escape Pod, IMHO.