Analysis of Harry's conversation with Snape in ch. 27.
"If he were a friend," Harry said, "all the more reason to forgive him."
Possible Snape thoughts: "He implies that I wasn't even a friend of She. How dare he!?" ... consideration of different ways of mutilation ... then "Oh! He can't possibly be like his mother. She had a very high standards for Her friends. Maybe his stepparents taught him this indiscrimination of friends."
"She was shallow"
"SHE was shallow!? ... But She married that brat Potter. Was Her standards high after all? Maybe not. And I gave all the power I could have for her..."
So I think Snape became misogynous. Thus Alissa's affection became irritating for him. I don't know what implications it will have for storyline however.
Edit: Analysis is done by Type 1 processing with Type 2 postselection, so no justification is given. :)
Edit: This hypothesis seems to be insufficient for explanation of emphasis on "wrong" in Aftermath 2, maybe there's something more.
Edit:
"Wrong" can mean, that she was aware, that Snape isn't kind of person young woman is supposed to crush on. I'm not sure that this is true for Slytherin. Anyway Snape isn't handsome guy, it's not deserve emphasis to hint that.
"Wrong" can mean, that she feels it's bad for her to show affection now. Fits my hypothesis, but not wording "There was probably something really wrong with her...", which imply that she knew it all the way.
Some part of puzzle seems to be missing.
This hypothesis seems to be insufficient for explanation of emphasis on "wrong" in Aftermath 2, maybe there's something more.
The "wrong" is presumably that the wizarding world isn't much familiar with, or accepting of, urges tending towards BDSM. A student of her age would be unlikely to be familiar with the idea of such a thing not being "wrong", given their lack of internet access. ;-)
Update: Please post new comments in the latest HPMOR discussion thread, now in the discussion section, since this thread and its first few successors have grown unwieldy (direct links: two, three, four, five, six, seven).
As many of you already know, Eliezer Yudkowsky is writing a Harry Potter fanfic, Harry Potter and the Methods of Rationality, starring a rationalist Harry Potter with ambitions to transform the world by bringing the rationalist/scientific method to magic. But of course a more powerful Potter requires a more challenging wizarding world, and ... well, you can see for yourself how that plays out.
This thread is for discussion of anything related to the story, including insights, confusions, questions, speculation, jokes, discussion of rationality issues raised in the story, attempts at fanfic spinoffs, comments about related fanfictions, and meta-discussion about the fact that Eliezer Yudkowsky is writing Harry Potter fan-fiction (presumably as a means of raising the sanity waterline).
I'm making this a top-level post to create a centralized location for that discussion, since I'm guessing people have things to say (I know I do) and there isn't a great place to put them. fanfiction.net has a different set of users (plus no threading or karma), the main discussion here has been in an old open thread which has petered out and is already near the unwieldy size that would call for a top-level post, and we've had discussions come up in a few other places. So let's have that discussion here.
Comments here will obviously be full of spoilers, and I don't think it makes sense to rot13 the whole thread, so consider this a spoiler warning: this thread contains unrot13'd spoilers for Harry Potter and the Methods of Rationality up to the current chapter and for the original Harry Potter series. Please continue to use rot13 for spoilers to other works of fiction, or if you have insider knowledge of future chapters of Harry Potter and the Methods of Rationality.
A suggestion: mention at the top of your comment which chapter you're commenting on, or what chapter you're up to, so that people can understand the context of your comment even after more chapters have been posted. This can also help people avoid reading spoilers for a new chapter before they realize that there is a new chapter.