It's hard to use restraint in a life or death situation. Especially if you train to go all out! In the excitement and adrenaline rush it's hard to just turn off the switch! Especially when life or death situations most often happen in the blink of an eye. And coupled with the fact that often times, you will experience a distortion of perceived time.
But sometimes that's what you have to do in order to remain on the good side of the law.
In this case, and especially with Castle Doctrine, I would say that Inside The Store, he was good to go!
Once he left the store and began pursuing the offender, Castle Doctrine Protection Ended!
Now personally, I'm on the side of the Store Owner/Manager... I don't like seeing criminals get away only to continue on their potentially murderous life of crime... But once the crook left the confines of the store and fleeing the scene, he really was no longer an immediate threat to the owners life.