I can well imagine Hermione getting a phoenix. Her potentially resulting self-sacrifice could well be a climactic point in the fic, in fact. Its effect on Harry would be interesting to see, too.
But Hermione isn't really rational, she's just intelligent. I don't think she can perform a feat of astounding rationality in this fic, as you are suggesting. Her idea of morality is flawed and naive. If I imagine her going to Azkaban and destroying it, it would be for decidedly uninspiring reasons to me, as a rationalist.
No offense (and I'm a boy so quite probably biased about this, fair warning) but are you sure you know what girls are like in real life? I know in a utopian world there would be no gender stereotyping, but in my honest experience, even as someone who strongly wishes stereotypes would all burn and die, girls in schools do gossip, and stress about relationships, and quite possibly are prone to sensitivity and preoccupation about love, even if it is culturally rooted.
Just wondering I guess if you've been so successful in emancipating yourself from that stereotype (congratulations on that) that you've ended up with unrealistic expectations of what is actually normal for girls.
That said I don't know you and don't want to come across as though I'm certain of what I'm saying either, just reporting on my brain's response to your comment.
EDIT: Typo fix
I did not mean that to be a Tardis, that is not what a Tardis looks like.
Eliezer, in the author's note.
Or making the stone has some mental prerequisite, like casting Avada Kedavra or the True Patronus. One, in this case, which Voldemort cannot meet.
I can confirm this works for me, in Google Reader (and my thanks to you also).
I...imagine you can't read the mind of any sleeping person.
Penalty for incorrect use of the word 'literal'.