Last night Damian Conway talked about Lingua-Romana-Perligata as part of his "Fun with Dead Languages" talk. He makes the point that Latin's suffixes don't constrain the word order. Given Harry's dream of destroying Azkaban and Dumbledore in Ch 79 muttering strange incantations that sounded not quite like Latin and echoed in their ears in an unusually creepy fashion, maybe Latin provides a larger space to search for a mnemonic phrase that the Source of Magic will match and action, than languages with a more constrained grammar.
There's also
"Um..." Harry said. "If there are any spells you can cast to make sure no one's listening to us..."
Professor McGonagall stood up from her chair, firmly closed the outer door, and began taking out her wand and saying spells. [...]
Professor McGonagall finished a spell that sounded a lot older than Latin, and then she sat down again.
Not to mention the Sumerian Simple Strike Hex. Mahasu doesn't sound much like Latin.
EDIT: New discussion thread here.
This is a new thread to discuss Eliezer Yudkowsky's Harry Potter and the Methods of Rationality and anything related to it. With two chapters recently the previous thread has very quickly reached 500 comments. The latest chapter as of 17th March 2012 is Ch. 79.
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: one, two, three, four, five, six, seven, eight, nine, ten.
As a reminder, it's often useful to start your comment by indicating which chapter you are commenting on.
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: