I don't have time to read the whole thread at this point, so what I say may have already been covered.
First, self defense does not usually apply to property. I know of no jurisdiction in the USA that would allow that, but stand to be corrected if there is one. If I shoot a person trying to set my house on fire, and I and my family are in the house, I can make a good arguement that I am not defending my property so much as myself and my family. Defending my family is not self defense, but most state laws allow defense of someone you are obligated, or allowed to defend, as justification to use deadly force against deadly force. But just to defend property, it isn't going to be a justification for using deadly force.
Bill, if you hand someone a knife and they attack you with it, legally you can reply with deadly force if you have no means of retreat. Practically, you would probably be made to look pretty stupid in court, as to why you handed someone a knife. You would also probably have to explain why you had the knife if there was any question as to that legality. If you weren't authorized to have the knife, you might find yourself labled a felon participating in a crime, and not have any defense. And if the local law, as most, require a proof there was no retreat, you will have to answer for that, proving you had none.
As to retreat or using a 2x4 to begin with, I would need more facts, such as was she in a position where she felt she had to protect her brother or herself. If so, some jurisdictions allow that a person of small stature, or facing someone who appears to have superior fighting ability and the inclination to use it, may use deadly force. They will have to convince a DA and/or a jury they feared for their life, or the life of someone they are authorized to protect, and had no retreat. Some allow that a victim fearing they could not escape an attack or imminent attack, for instance, being disabled, or not a fast runner, might be justified in using deadly force in defense. If it isn't very obvious, they still may find themselves defending it in court.
Once a thief, or even an assaulting attacker, breaks off the commission of the crime, deadly force is not justified in any jurisdiction I am aware of. If she reasonably feared her brother had been killed, or in fact knew he had been, I don't know that most DA would prosecute. However, as I have read up to the end of the second page of the thread, that wasn't so. When the thief/robber broke off his attempts/attacks, he was still game for a citizens arrest, but not to be shot and killed. Worse, he not only broke off his attack, he was fleeing. She could have stopped and called the police. She had no legal right to shot him in defense of property, even though his possession of the property may have constituted another crime besides theft.
Sorry for the long post, but I wanted to cover everything I thought was necessary.