I think that Quan's actions at the end of the novel indicate how far he has come in his reflection about the war and his place in it. At the start of the war, when Quan, Bien, and Luong, enlisted for the war, there was so much patriotic nationalism. The fervor and belief in the authenticity of what was being done is in stark contrast to the feelings he has towards the war effort now. Quan understands that war is not the singly force of unity in which all individuals subjugate their own desires for a greater good. Quan has seen that individuals have manipulated the war for their own benefit, abused the power possessed in order to gain more control. He recognizes this in his girlfriend from the village who has been impregnated by a government official and then discarded when she is not needed. Through events like this, Quan has recognized that the soldier is the fundamental tool of the powerful in the machinery of the war.
It is for this reason that Quan does not execute the American. Quan recognizes that the American and he are the same. They are both tools by those in the position of power to advance an agenda that is not theirs in the first place. The soldier, regardless of both sides, suffers the most, sacrifices the greatest, and receives the least reward. This thinking has replaced the singular focus that Quan had at the start of the war and represents how he has changed over the course of his experience. His values are more humanistic in scope, reflecting the war is a dehumanizing experience for both sides. No flag or army uniform can conceal the stress and pain of the solider and Quan realizes this at the end of the narrative.