This one is actually the least crazy of the lot, I think - the super-Patronus works on the principle of love for all human life. Someone who casts it ought to be damn near incapable of murder, and if the principle could be explained to the Wizengamot without ruining everything, the fact that Hermione managed it would actually constitute exculpatory evidence.
Love of all human life does not translate into an inability to do math or unwillingness to murder.
As well, it's not clear that guilty Hermione feels good enough about herself or all human life that she would be able to cast it.
It's not a likely case, just less IMO unlikely than the others I listed. I'd put the odds at perhaps 10-20%. The rot13'd answer is the one I think is solidly the most likely.
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: