What were the rest of his words? What exactly did he say to the po-po? Without knowing exactly what he said to the police or what actual actions the "alleged" perps took, one can not fully and appropriately judge the outcome. Some people say stupid things not knowing they can be misconstrued or taken out of context.
Did the bad guys know he was there in the "secure back room"? Just because they threw bricks through the windows does not mean they were a threat to him or threatening him. Not all states have "stand your ground" laws. Some require you to run away from a threat if there is the opportunity to do so. (I did not write the laws so don't blame me.)
Were the BGs too busy breaking in to the cash register to know he was there when he poked his head out? Did he shoot the guy in the back? The side? In the butt? Any of those would suggest that the employee was not in immediate danger or being threatened when he pulled the trigger, hence the reason for the Malicious Wounding and Reckless Handling of a Firearm charges.
Depending on your local laws, just because an "alleged" bad guy is in your home or place of business, it does not automatically give one the right to shoot them. Legally, there may be specific actions that they would have to take/make in order for you to be able to shoot at them. Again, don't like the laws, change them!
Another story indicates the employee "
had a "protective order" against him, which may prevent him from possessing a gun." Was the gun his or was it the property of the store owner? Without knowing, how can question the legality of those charges.
If you are making a "final" call based on the very limited details include in these stories, you are rushing to judgement and should really consider broadening your critical thinking skills.