I wouldn't include them because they are justifiable homicides in self defense. The person defending themselves wasn't given a choice. They could shoot and live or not shoot and die. Basic self defense is as much a right as owning a firearm.
A criminal or sane person using a firearm to commit a crime has a choice.
for the basic definition of saying that a homicide is a person who has been killed by another person I agree with that.
For the purposes of pro gun vs. anti gun argument excluding them gives us a better picture of who is committing crimes with firearms. Those should be the focus of any legislation, not folks who use firearms lawfully. For that purpose there should be a category of justifiable homicides. I am not sure but I think in the Uniform Crime reports this information is listed as well. Been a while since I have used any data from them.
As a society the overall homicide rate may gave us an indicator of levels of violence. We know that simply passing laws have very little effect on that violence level unless you target the offenders. In fact violence seems to be on the rise in our society. That may stem from 9/11 with federal law enforcement, especially the FBI, being focused on terrorism.