Exceeding authority under a castle law
Note that calling the police immediately afterward, as here, is a very good idea -- not calling the police as soon is one safely can is a very bad idea, suggesting guilt -- but it probably won't be enough in this case to save this guy from some jail time.
Ignatius Piazza, a self-defense trainer, has a good collection of videos on this case. Local TV station KRMG has a version with the prosecutor narrating the surveillance video (a much better but obviously biased narration).
Not mentioned in these videos is that the armed robber who ran away was also and quite properly charged with murder -- what is called a felony murder, because he committed a felony that led to a death, even death caused by a victim of that felony as here.
Technically, all the Oklahoma statute does is shift from the defendant the burden of proving "a reasonable fear of imminent peril of death or great bodily harm" when killing somebody who has forcefully entered a dwelling or vehicle -- instead the prosecutor must prove that the fear was not reasonable. Here, the burden of proof does shift to the prosecutor, but, again assuming the facts are as he claims, he should be able to prove beyond reasonable doubt either that the pharmacist in fact had no such fear, or that any such fear of harm from an unconscious man was unreasonable.
Even assuming the injured robber had regained consciousness, a much better course of action would have been to have the women at the back of the store call the police and to hold the gun to the robber's head until the police arrived.
I strongly second Ignatius' advice that if you own a gun that you may one day have to use for self-defense, that you take a good training course. Military training is not sufficient for this and indeed may have led this pharmacist, a military veteran, astray. Military doctrine is a very different thing than the civilian law of self-defense and the castle doctrine. I do take issue with Ignatius' simplistic description of a supposed "universal" rule for when self-defense is justified. Some jurisdictions allow far more defense of self, others, and persons within dwellings or vehicles than he describes (especially castle doctrine and stand-your-ground states), and some allow less. If you are going to have a gun around for self-defense, you should learn the laws of your own state, province, or country and you should train yourself accordingly. The laws vary widely. If you aren't willing to learn the laws and train accordingly, as this pharmacist apparently failed to do, you shouldn't keep a gun. By using a gun against criminals you are, morally speaking, deputizing yourself as a law enforcer -- a very good thing, since the police usually can't get there in time to protect victims, but a status that comes with a moral responsibility to train yourself in how to legally use a gun. Self-defense and castle laws give you this authority; misusing these rights is what the prosecutor properly (again assuming his version of the facts) calls "exceeding authority" and thus murder. Note that under the recent Heller Second Amendment case, self-defense and defense of others is a primary justification for our right to own a gun in the first place in the U.S.
The castle doctrine under common law, as well as the quite related knock-and-announce rule for law enforcement, comes from Semayne's case: "That the house of everyone is to him as his castle and fortress, as well for his defence against injury and violence, as for his repose...if thieves come to a man's house to rob him, or murder, and the owner or his servants kill any of the thieves in defence of himself and his house it is not felony, and he shall lose nothing." Modern castle statutes, such as Oklahoma's, often also apply this doctrine to businesses and vehicles. The Wikipedia article on the U.S. castle doctrine has a list of states with stand-your-ground laws and castle laws, with links to the statutory texts.
By the way, political scientists who define governments as entities having a "monopoly of force" are idiots. I just thought I'd get in that shot of my own while I'm here.