It is easy to demonize people who have harmed us directly or indirectly. With regard to the book Flight, it could have been easy for Sherman Alexie to demonize the "Indian Tracker" Gus, rather than portray him as a feeling person. If Zits had been inside another body in that scene, particularly the body of another First Nations person, it could have been easy to just take the character of Gus as a hateful person with no conscience. I think that Alexie chose to put Zits into Gus' body to show that acts of hate and war can't just be reduced down to mindless action in order to make it easier to understand.
A running theme in the book was also to observe and possibly re-write history and Zits' own future. By having Zits control Gus' action, Alexie both demonstrated conscience on the part of Gus, who joined the military because he wanted to help people. War and conquest are not summarized in one broad stroke of action, and have always involved many small acts which add up to the big picture. Gus' kindness in helping save Bow Boy and Small Saint shows these subversive actions which are often left out of the telling of history.
Zits learns throughout the book that his actions affect not just those immediately around him, but their friends and families and so on.