I realize it was self defense when John killed Zipper, but wouldn't he have been investigated or something for killing another cop? It's not like there were any other witnesses (that I recall anyway). Would they just be like "oh, it was self defense? Okay we take your word for it." I thought it was kind of strange that it was just left at Zipper being dead and that was it. But then, I guess that would have slowed down the movie if they had to go into a whole investigation. Right?
There were actually two other witnesses to Zipper's death. When John retreats to Zipper's new motorcycle, you can see other residences in the background & two people emerging. The argument escalates to a degree audible enough for them to hear the shouting. Zipper then begins shooting. One of his shots actually strikes the first bystander, who falls. The second bystander then runs to the first one's aide. It happens when John says "You're shooting people, Zipper!" ( or words to that effect ). Just look over Robert Blake's shoulder during the scene & you'll see it all. The camera even zooms in to make it more clear, but it happens very fast. Robert Blake's body is in most of the frame when them moment occurs, potentially distracting the viewer's attention from these important details.
One can easily assume the person Zipper shot didn't die & subsequently ( along with the second bystander ) corroborated John's report of the unfortunate incident.
There is the possibility that John never would have fired had Zipper not endangered the lives of these two people.