There is no such thing as "shooting to incapacitate" even if you can put the gun directly on the point you're trying to hit. Any bullet entering the body in any way is either potentially lethal or nearly harmless. The belief that there's any such thing as a disabling shot does nothing but lower the engagement threshold. If you shoot someone, you are attacking with lethal force, and if they happen to stop being a threat without dying that's just good luck for both parties.
As to this specific incident, unless there's a video of the shooting we don't know exactly what happened. The best procedure for this situation would be to make no moves other than what the officer directly requests, and to comply with those requests by loudly and clearly announcing what you are doing and doing it very slowly. If you are pulling your gun out in response to a police request (not an unreasonable thing for a cop to request as it reduces his risk for the duration of the stop), you should use no more than three fingers and grip it as far from the trigger as possible, to make absolutely sure that you are not presenting a threat. If the person in question did operate among these lines, the cop is clearly in the wrong. If not, it becomes bad judgement at worst.
These are the procedures I would use if stopped while carrying, and if I didn't I would consider it to be my fault if I got shot. I fully support the right to carry, but if you choose to do so you commit yourself to a certain standard of care because you are in possession of an object that is deadly if mishandled or misused. Any concealed carry class that doesn't impress this point should be shut down.