I just consider it to be a point of view. The Imperium will emphasize on the negative aspects of Khorne, while a follower of chaos will see all those aspects like martial honour etc etc. If you're playing Black Crusade, you read about the negative side of the imperium as well. In the eyes of a follower of chaos, the imperium are the bad guys. It works in 40k because there is no true good or evil, it's just all grey zone.
So basically, both sides are right.
Edited by Gridash