I thought the point was to show the dehumanizing aspect of war, to show how the military warps people into doing acts they would never have dreamed of before. That was the great irony of the first part. The sergeant drilled into Pyle the all-importance of killing the enemy when you see him because you were told to do so. And that’s what Pyle did. He killed the enemy when he saw him–the “enemy” being the sergeant and what Private Pyle had become. In the end, he was a perfect product of basic training, a machine-like Marine.
That set the stage for the remainder of the film. Although Joker is not a “perfect” Marine like Pyle, even he could not overcome what training and war had made him.