When the narrator views the body of the Burmese man who had been crushed to death in a crucifix-styled posture, he has an overwhelming attack of conscience. The narrator realizes that just like the Burmese man, the elephant had been a crucified, as well, and it does not pacify the narrator that his killing the elephant was within legal parameters.
The narrator realizes that law and conscience are often not compatible. He is there in an official capacity and is hated for it by the Burmese. He equally has hated them for their hostility. Yet, when he allows his conscience to surface, he understands that he is part of the structure that is there to oppress the Burmese. The fact that he holds a position of authority does not necessarily make it a moral duty. This is true of his killing the elephant. He did not want to lose face in front of the Burmese, and he was legally justified in killing it, but morally he knows that it was actually morally wrong.