It sounds like you might be mistaking Eliezer's role in this, and mistaking your desires for desires we can reasonably assign to Eliezer.
This isn't something that happened to the HP&tMoR version of Hermione Granger, this is something that Eliezer, the author did to the HP&tMoR version of Hermione Granger.
He did it for a reason. He's almost certainly been planning it all along. If it made him sad then it first made him sad quite some time ago. He's not feeling the surprised dismay you have today.
He wanted this.
He wanted the words written on the page to be written on the page, yes. That does not, strictly speaking, mean that he wants Hermione to be dead. He's been known to play with our expectations before, after all.
Edit: To clarify, this is almost certainly wishful thinking talking, and I acknowledge that. But a guy can dream.
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 88-89. The previous thread has passed 500 comments.
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: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18.
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: