Oh, yea, I completely agree with that. If somebody broke into my house, I would feel threatened and I would protect myself. I, however, wouldn't chase them when they would try to run away (like this farmer seemed to do). I think that's the difference between defending yourself, and beating the crap out of a person when they're already running away or are down... So, self-defence should be allowed, but ONLY when it's self-defence. It stops becoming self-defence when your safety isn't in danger anymore...
So whoever would defend themselves, or hurt an intruder when their life was in danger shouldn't be accused of murder, or injuring a person or anything like that. But, if they chased the thief outside when they were trying to get away (not endagering you anymore) and then beat them up some more, then I see no problem with putting this person up for a trial.