For me the most natural explanation of the dojo incident is that Quirrell/Voldemort pulled a Verbal Kint. The setup is just too similar to be accidental. If you haven't seen The Usual Suspects (you should), that means ur vzcebivfrq gur fgbel ba gur fcbg gb znxr rirelbar srne uvz naq gb uhzvyvngr Uneel. I'll be quite disappointed if Eliezer's eventual explanation isn't as good as this one.
My understanding was that the story was true as stated: Voldemort showed up, destroyed the place, then calmed down and realized Quirrell now had the only remaining copy of the information he was looking for, so he set up some contingency to eventually put himself in Quirrell's body with the martial-arts skills intact.
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.