I agree with your assessment of how powerful Perenelle/Flamel (side note: need a good portmanteau a la Quirrellmort) should be, having been able to outwit Baba Yaga in her sixth year and then having six hundred years of excellent leverage to accumulate lore and also maybe play with what the stone can do.
That objection notwithstanding, the most plausible non-Voldemort killer would be Bellatrix, using her superpower of very strict obedience to orders like "Just use AK and do not hesitate for any reason".
It's not Perenelle, it's still Baba Yaga, who killed a sixth-year dark witch, stole her identity, and faked her own death.
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 116.
There is 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.)