The points you noticed confused me as well. My (very strong) gut reaction was that obviously Dumbledore is behind it all - he is the one with most control about the wards, and he is the one who gives both the readers and the participants of the meeting the information tha the wards point to the Defense professor as culprit. Also, the line about the heir triggered a mental alarm.
As I said, this was a gut reaction, and it has been quite some time since I read the rest of the story - this is just based on chapters 90 to 94, and the general impression I got from the story so far that this Dumbledore is definitely very different from canon Dumbledore.
This is a new thread to discuss Eliezer Yudkowsky’s Harry Potter and the Methods of Rationality and anything related to it. This thread is intended for discussing chapter 93. The previous thread has passed 300 comments.
There is now a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author’s Notes. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18,19,20.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: