Huh. My first thought was simply to argue that a work of fiction is rarely improved by attempting to make it meet certain moral standards; The Kreutzer Sonata isn't any less great for espousing despicable beliefs, and plenty of terrible novels inspire laudable ideas of human society. So, if artistic quality and moral quality are unrelated, better that an author write what comes from their heart rather than attempt to teach what they haven't yet interiorised themselves, and risk coming off as insincere or overzealous.
However, MoR is ostensibly meant to be an educational and inspirational story as much as an entertaining one, so in that particular light the suggestion carries more weight. Even so, it wasn't Eliezer's decision that the fated hero be male and the well-meaning-but-over-her-head companion be female. Perhaps more importantly, had Ron kept his canon role instead of being replaced by Draco, there would have been a second, male WMBOHH companion, Hermione's frustration would not have been framed in terms of perceived sexism in the first place, and there probably would not have been a S.P.H.E.W..
Even so, it wasn't Eliezer's decision that the fated hero be male and the well-meaning-but-over-her-head companion be female.
Actually, insofar as he decided not to gender-flip everybody or change the prediction, he did decide to make the fated hero male and the companion female.
Not that I think he should have done otherwise, all things considered, but this kind of argument annoys me in general.
Update: Discussion has moved on to a new thread.
The hiatus is over with today's publication of chapter 73, and the previous thread is approaching the 500-comment threshold, so let's start a new Harry Potter and the Methods of Rationality discussion thread. This is the place to discuss Eliezer Yudkowsky's Harry Potter fanfic and anything related to it.
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. The fanfiction.net author page is the central location for information about updates and links to HPMOR-related goodies, and AdeleneDawner has kept an archive of Author's Notes.
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: