The absolute LAST thing the homeowner should be worried about is getting his gun back. He should be worried entirely about staying out of prison.
The article is woefully lacking in detail so this is just based on ONLY what is in the article, and is only my opinion:
If absolutely everything in the article is correct, and there are no other significant facts not mentioned, then the homeowner is probably in big trouble. Burglarly is indeed a felony and so a shoot while someone is committing burglary would likely be legal. However, the second the attempted burglary stops, unless there is another attempted felony taking place, you can NOT SHOOT. So if the homeowner was holding one or more of the burglars at gunpoint outside his home after confronting them, and they had dropped all weapons, then unless they were trying to run away with $1000 or more of his property (felony theft) he couldn't legally use deadly force. As a criminal the best response in such a situation is to drop everything, hold your hands above your head, turn around, and walk slowly away until out of sight around a corner, then run like hell. Very few people will be stupid enough to shoot an unarmed man in the back. As a homeowner, shoot them while they are inside, or if they are outside tell them they have 10 seconds to get out of your sight, and that you will kill them if you ever see them again. You do not want to be stuck holding a gun on them for 10 minutes waiting for the police to arrive, then having to deal with the police late at night when they are tired and nervous and you have a gun in your hand.
That being said, what really matters is whether the local prosecutor has an election coming up and whether he feels coming down hard on this guy will get him more votes or less. Sadly, almost all self-defense shootings that aren't definitely 100% good end up being prosecuted more based on politics than what is right.
In this case, honestly I don't know what happened and don't know whether the homeowner should be prosecuted or not. I feel bad for him that he had to be in this situation at all, and if he is prosecuted I hope it is for the lightest charge they can get away with, but sadly he may still be prosecuted if the kid was just trying to run away or something.