An attorney I saw interviewed about this story said that Missouri's Castle Doctrine Law applies to "anything with a roof" on your property. Therefore he was not charged for the shooting itself.
Reporters still can't be bothered to learn anything about self defense law.
The Castle Doctrine, like Stand Your Ground, only refers to whether there is a duty to retreat before using deadly force. It doesn't address the other elements of self defense, which still have to be met for the shooting to be legal.