So to the first part, lasting amount of good from a long-term consequentialist standpoint isn't the same as how much impact someone has. And if one is trying to think of long-term issues then Harry has also discovered how to destroy otherwise unkillable creatures, and has set Draco Malfoy on the path to redemption. Even if Harry dies tomorrow, the total utility of there being one less dementor in the world will add up a lot over the long term. (In canon dementors can reproduce, but I strongly suspect this isn't the case in HPMOR.)

The main change between HPMOR and canon is the hugely increased power, intelligence, capability, and potential for evil of the protagonist, who yes, we assume has a penis.

This isn't the only change. There's also a massive increase in power, intelligence and capability of the antagonist, who, yes, we assume has a penis. There's a massive increase in Dumbledore's genre awareness and awareness of the cost of his actions to others, and his general power level (using Time Turners), who yes, we assume has a penis. There's a massive increase in Draco Malfoy's manipulative skill, who yes, we assume has a penis.

Moreover, while some female characters have become more interesting (Daphne and Tracy are obvious examples), they still are orders of magnitude less important. And there have been other possible options which could have been interesting. For example, rather than just having Petunia as a helpless housewife, while her husband is a professor, Eliezer could have had written something where she was also an academic, or a successful businesswoman, or a lot.

If your mind pattern matches this as an affront to women everywhere, you have a problem.

I'm not sure if this is a strawman or a genuine failure on my part (and possibly others who are concerned) to explain our concerns. No one anywhere in either this discussion thread or the previous HPMOR discussion thread has made the argument "that this is a general affront to women everywhere". And I'm pretty sure that I don't believe that. (Introspecting quickly, it is possible that my stated and actual beliefs don't align. However, if I did think that it was such an affront I douubt, I would have used as my interesting icebreaker fact last Friday that I had cosplayed as a character from a Harry Potter fanfic, and then used that as a way of getting an opportunity to tell people to read Methods of Rationality.)

To state it more explicitly problem is that this is a set of not great role models. My guess is that close to half the readers of HPMR, or certainly a large fraction, are female, and likely pretty young, which makes them impressionable. So, subtle (or not so subtle) differences in what male and female protagonists can do are important. And if some young girl gets pushed slightly over the edge by this into not becoming a chemist or a biologist, or just becoming interested in rationality, we all lose. Moreover, if part of the goal of the story is to get people as a whole interested in rationality and Less Wrong, then for women of all ages, having a substantially weaker female lead is going to make it harder for them to identify with the characters, and all the more so, when that weaker female is (apparently) killed off without even saving anyone in the process.

There's a lot of room for legitimate concerns without thinking that this is an affront to women everywhere.