About Harry’s darkside. It seems new and weird that his darkside can be hurt by Hermione’s plight. Last time he went over to his darkside strongly (after dementor exposure), he ended up in a state where he hated everyone he cares about and only came out because he didn’t know how to respond to her kissing him, not because he cared.
This is in fact exactly what happened:
Without even thinking he was trying to flee inside himself, flee into his dark side, pull the cold rage over himself like a shield. It took too long, he hadn’t tried to go fully into his dark side since Azkaban. And then when his blood was something like cold, he looked up again, and saw Hermione in the chair again, and discovered that his dark side knew nothing about how to deal with this type of pain, it pierced through the coldness like a knife and didn’t hurt less in the slightest.
This is in fact exactly what happened: