The rehabilitation program is itself brutal, with the intent of brainwashing Alex into civility by implanting in him an artificial conscience. The Yugoslav government knows that shocking images of violence can influence societies, too. Of course, we have no way to tell whether it was NATO, the Serbian military, or the KLA that inflicted the gruesome wounds, but somehow it doesn't matter all that much. The people are still equally, horribly maimed or dead. In this case there is no good, righteous side.
All parties are wrong and guilty for the terror they rain down on the people in the Balkans.