What should change?
"That being said, an argument could be made as to which gun killed the poor guy if him having a firearm prompted the officer to shoot him."
No the argument can't be made, there's no question the officer killed him with his gun. These types of trigger-happy officers will decide your wallet looks like a gun, a pack of smokes looks like a gun, a phone looks like a gun. A few years back locally, a police officer shot someone through the heart who was in their own art studio (at midnight) talking on the phone. Initially he claimed he thought the phone was a gun, then said he saw the door open, decided to just go in and flinched when someone was standing right there.
Several things need to be done:
1) This "police having other police's back" type nonsense has to go. Comradery and so on? Yeah, this is fine. Covering up for officer misconduct? This has never been a good thing, it has always tarnished reputations of departments involved (due to rumors and so on); it's now the 21st century, so these coverup attempts will be completely unsuccessful, and it won't be rumors tarnishing the department but proven fact of misconduct and coverup. (In the art studio example, there was no attempt to cover up.)
2) Make sure officers do follow their training. Some few will just plain be dirty, and they've got to go. Some aren't "dirty" but just don't have the temperament for it, they're too high-strung. Plenty of others just don't quite follow procedure... which doesn't usually lead to any problems, until it does. (In the art studio example, the officer went in alone when procedure was to go in with backup; both for officer safety, and to keep the officers calmer (since they have backup) and so less likely to make mistakes.)
3) The mentality. There are definitely some departments with an "us versus them" mentality; the police tend to not be respectful toward the public, the public know what they'll get interacting with the police and are not respectful either. The officers tend to be rather high-strung and nervous ("us versus them" remember); the public knows if they are stopped they'll be treated like a criminal, so they're nervous. The police are trained to be suspicious when the person stopped is nervous, so this makes them more nervous... On the other hand, there are departments that take "protect and serve" seriously, they want to reduce crime while recognizing they shouldn't interact with the general public as though they are all potential criminals. They treat the public with respect, and are (usually) treated with respect in return. It makes their job easier and less stressful, and they stress the public less. I'm happy to say, locally the local PD and the state patrol both tend to be reasonably friendly.