The legal grounds for a claim of self-defense varies a lot from state to state. I'd say (but can't be sure) that in the majority of jurisdictions, you lose the right once the threat is gone. So, if you get mugged and pull a Vulcan chain gun from your trench coat and the mugger runs away, you can't chase after him firing 6000 rounds per minute. If you fire at him BEFORE he runs away, then you're probably free to turn him into a fine pink mist. That's where they fucked up. They needed to hit him with the first shot BEFORE he tried to get away. Otherwise it goes from self-defense to a citizen's arrest. In that case, you have the same limitations as the police in the sense that you are not allowed to use excessive force. But if the store owner wasn't the one firing the shot, the case against him will probably be dismissed. He'll just have to file a motion for a summary judgment and he should be fine.
I bet they will end up paying thousands of dollars to and close shop trying to defend again against this.
It's real simple, if you sit on a jury for a case like this, you never convict (criminal), or side with the plantiff (civil). A criminal has NO rights, nada, none. I don't care if he has turned around and started to leave, kill the motherfucker and I will not convict you.
That's what I'd do, but you'd be amazed at how "compassionate" some people can be when it's somone else's money.