Here's what I think will happen:
Zabini stuns himself in the name of Sunshine to create a tie. And here's why:
1) The rest of the school is very partisan about their favorite army, so it's not likely that many are betting on a tie. Zabini (through a proxy or otherwise) put all of his chips on "tie." So he will return to Hell a much richer Prince of Darkness.
1a) "Aftermath" scene: Hogsmeade. Zabini meets his broker. Hogwarts is basically a closed economy, and Zabini has now walked off with the lion's share of the student body's disposable income. He plunks his Bag of Holding on the table. "Take this and convert it to Muggle money. Then go buy unmarked silver bullion..."
2) The three Generals are tied for Quirrell points. Given what we've seen of him in this chapter, Zabini is probably in fourth place, and not too far behind. How many Quirrell points will he get for getting all three generals to play according to his plan? We see Harry and Hermione accepting, and per the Prisoner's Dilemma thing, Harry and Draco had to synchronize their moves ("cooperate") to have a chance against Hermione. This would mean that Draco is also more or less following Zabini's plan. Zabini was able to steer the battle to his personal chosen outcome, so he (as an individual) wins the battle. The betrayal rules+scoring are set up to favor individual objectives rather than army loyalty/collective goals/unity. Zabini has realized this, and acted accordingly.
3) After collecting Quirrell's wish from his come-from-behind victory (which provides a "practical" demonstration of the 2-4-6 Test, since no one, Generals included, expected Zabini to have his own victory conditions), Zabini goes to Dumbledore's office. "Well done, Blaise!" Dumbledore says. "I suppose you're here for your wish..." That is, Dumbledore has offered Zabini a wish if he could steer the battle to a tie, since that would stop a Hogwarts equivalent of a football (soccer) riot, which would be likely if one of the armies won.
4) At the Christmas feast, Dumbledore rises to announce that the three armies are being merged into a Hogwarts Army, and starting at the end of January, the HA will compete in three-way battles with Beauxbatons and Durmstrang. Per the experiment mentioned earlier with the "Eagles" and "Rattlers," the Hogwarts students are united against external foes. He and Quirrell allowed the Headmasters of the other schools to watch the battles using Quirrell screens, and their staffs liked the idea. The mock battles use more magical skills and incorporate more students than Quidditch, and are thus a better encouragement to learning. New rules could be applied to future battles. "You may use any magic item you can make (under teacher or senior-student supervision) in your battles, providing it's not dangerous." "You can use any Potion you can make," etc.
Predictions?
Regarding the note of confusion Harry feels in Chapter 3: the Killing Curse "strikes directly at the soul", but in Voldemort's case it burned his body. More likely he never cast it at Harry Potter, and the burnt hulk they found wasn't him. He learned about the prophecy and, being smart, changed his plans rather than risk fulfilling it.
And the Source of Magic is a UFAI that optimizes the world into stories.
I hope all my predictions turn out wrong. What I want most from this story is to go on being surprised.
Update: Please post new comments in the latest HPMOR discussion thread, now in the discussion section, since this thread and its first few successors have grown unwieldy (direct links: two, three, four, five, six, seven).
As many of you already know, Eliezer Yudkowsky is writing a Harry Potter fanfic, Harry Potter and the Methods of Rationality, starring a rationalist Harry Potter with ambitions to transform the world by bringing the rationalist/scientific method to magic. But of course a more powerful Potter requires a more challenging wizarding world, and ... well, you can see for yourself how that plays out.
This thread is for discussion of anything related to the story, including insights, confusions, questions, speculation, jokes, discussion of rationality issues raised in the story, attempts at fanfic spinoffs, comments about related fanfictions, and meta-discussion about the fact that Eliezer Yudkowsky is writing Harry Potter fan-fiction (presumably as a means of raising the sanity waterline).
I'm making this a top-level post to create a centralized location for that discussion, since I'm guessing people have things to say (I know I do) and there isn't a great place to put them. fanfiction.net has a different set of users (plus no threading or karma), the main discussion here has been in an old open thread which has petered out and is already near the unwieldy size that would call for a top-level post, and we've had discussions come up in a few other places. So let's have that discussion here.
Comments here will obviously be full of spoilers, and I don't think it makes sense to rot13 the whole thread, so consider this a spoiler warning: this thread contains unrot13'd spoilers for Harry Potter and the Methods of Rationality up to the current chapter and for the original Harry Potter series. Please continue to use rot13 for spoilers to other works of fiction, or if you have insider knowledge of future chapters of Harry Potter and the Methods of Rationality.
A suggestion: mention at the top of your comment which chapter you're commenting on, or what chapter you're up to, so that people can understand the context of your comment even after more chapters have been posted. This can also help people avoid reading spoilers for a new chapter before they realize that there is a new chapter.