Hermione is the actual hero of the story. Every time rationalist harry makes a mistake he is acting against her direct advice. Her character literally exists to show off his deficiencies and his coming of age basically boils down to realizing he should be more like her.
For many reasons voldemort is an ultimately worthy adversary. Much of that has to do with Harry's biases that come from being too invested in rationalism. Since he considers himself above everyone he's ever met he longs to find someone he considers his better and voldemort fills this role. He wants a mentor so badly that he's willing to throw out his entire ideology to keep him. I think yudkowsky's portrayal of voldemort as the ultimate adversary to rationalism is better than pretty much any plot arc in the original story. Harry does ultimately completely reject voldemort so Im not sure how sexual violence, genocide, and mass murder as treated as forgivable. From the very beginning Harry is deeply concerned with human rights, his distractions and the path he takes toward achieving human rights in this messed up world is again an integral part of the story.
> The fact that he acknowledges at the very end that the characters he created are fools
I think this is my biggest issue with your characterization. Yudkowsky shows harry to be a fool from the very beginning, as you pointed out with the draco/ron stuff. With his dismissal of much of hermiones advice. He very consciously did not create harry as some ubermencsch character who can do no wrong. He shows that harry believes himself to be a parity of virtue, but that he very much is not until hermione's death.