The only plausible reason whoever killed Hermione hasn't killed Harry too is because they want him to remain alive. They could have, because Hogwarts security is no great impediment to whoever did this, and Harry isn't a genius in his sleep. They would have, too. Anyone who hates Hermione would hate Harry, too. He was summoned to help during her confrontation with bullies. He used legal tricks to intervene when she was about to be "kissed." He's obviously the bigger threat, and whoever killed Hemione should have some fear of vengeance from him.

Unless it's Voldemort, who knows that Harry is a horcrux, as in canon, and knows that in killing Harry he would injure himself. Quirrel knows that he has a telepathic link with Harry. As Quirrel told McGonagall, he is a wizard "almost" on the level of Dumbledore and Voldemort. The Quirrelmort theory posits one less extremely powerful wizard. Hermione was killed by a troll. In canon, that is Quirrel's signature. Quirrel is voldemort in canon.

Am I missing anything?