Now, I've only skimmed the first three pages, so forgive me if someone has already brought this up... but self-defense doesn't necessarily apply in this situation.
Putting aside castle doctrine for a moment, defending yourself is not a get-out-of-jail-free card for killing another human being. Quoting Wikipedia here: "[...] when the degree of violence used is comparable or proportionate to the threat faced, so deadly force would only be excused in situations of "extreme" danger. The defense would fail, for example, if a defendant deliberately killed a petty thief who did not appear to be a physical threat." (1 [http://en.wikipedia.org/wiki/Right_of_self-defense#Legal_status_of_self-defense])
Now bear in mind there is no mention of a weapon in the linked article. There is no indication of the degree of violence used, if any, on the part of the burglar. The article vaguely states the man "accosted" him. And what exactly does that mean? Let's try Wiktionary: "To approach and speak to boldly or aggressively, as with a demand or request." (2 [http://en.wiktionary.org/wiki/accost]) Or Merriam-Webster: "to approach and speak to often in a challenging or aggressive way" (3 [http://www.merriam-webster.com/dictionary/accost])
So the only thing the article says, and of which the only source is the man who could face criminal charges for his behaviour, is that the burglar approached him in potentially belligerent fashion. Everything else is the biased interpretation of the readers here, who empathize with the "victim" and demonize the burglar.
Also, let us consider that the college student did not stumble across the intruder, feel he was in danger, and reach for a weapon to defend himself. Before ever even confirming there was an intruder, nor what danger he might pose, he went directly for a very dangerous and quite lethal weapon, which may itself constitute mens rea -- malice aforethought.
Furthermore, the article says he "noticed the garage door was open". So he was outside the house, not in any immediate danger, but rather than go to a neighbour's house and call the police, or even to a payphone, he goes inside with the intruder? No, he goes and gets a lethal weapon, then he goes inside to confront the intruder. He puts himself in the line of danger through his own actions, and was obviously expecting to use violence as evidenced by the fact that he took a sword with him.
I'm soon going to have to address castle doctrine, so I'm going to point out more thing out regarding self-defense, in general. Even if you are attacked, and the person is using violence, and you have reason to fear for your life, there may be a duty to retreat. Going back to Wikipedia we have: "Some American jurisdictions require that a person retreat from an attack, and allow the use of deadly force in self defense only when retreat is not possible or when retreat poses a danger to the person under attack." (4 [http://en.wikipedia.org/wiki/Duty_to_retreat#American_law])
So, castle doctrine. Well, Maryland doesn't have any statutory laws covering castle doctrine. The only support for this defense is in case law. And if you haven't already guessed, it too requires you use reasonable force to defend your person. So what's reasonable? Going back to Wikipedia:
"1) The defendant actually believed that was in immediate and imminent danger of bodily harm.
2) The defendant's belief was reasonable.
3) The defendant used no more force than was reasonably necessary to defend in light of the threatenend or actual harm." (5 [http://en.wikipedia.org/wiki/Right_of_self-defense_in_Maryland#Self-Defense_.28MPJI-Cr_5:07.29])
"No more force than was reasonably necessary", eh? Now, call me crazy, but I think removing body parts and killing people would require he be in some pretty freaking serious danger to meet all three above requirements. All this against a person we don't know was armed, or even acting violently.
What about defending your property, though? Back to Wikpedia:
"1) The defendant actually believed that (victim) was committing the crime of (crime) in the defendant's home.
2) The defendant's belief was reasonable.
3) The defendant used no more force than was reasonably necessary to defend against the conduct of (victim)." (6 [http://en.wikipedia.org/wiki/Right_of_self-defense_in_Maryland#Defense_of_Habitation_-_Deadly_Force_.28MPJI-Cr_5:02.29])
The third one is the problem yet again. There was no other way to stop him from robbing you than using a samurai sword? Especially considering you were outside the house to begin with? You couldn't call the police? You couldn't get your neighbour to help? You couldn't use any weapon less deadly than a sword? Really?
Let's be honest on what really happened. Burglar breaks into guy's house. Guy is scared/pissed off. Guy gets a sword, freaks out when confronted by burglar, and maims and then kills him. That's not self-defense. That's not even close. The burglar was wrong, but he didn't deserve to die because of it. The student should go to jail. The end.