I'm not quite sure the extent to which you're right or wrong, but a few points: 1- Once Minerva sees what she does of Harry's talk with Draco (realistic or not), it seems plausible she'd be impressed and give him slightly more slack because of it. In addition, once she begins to believe Harry has been abused it is possible she'd feel sorry for him. 2- Prior to this, I agree that she should have been significantly more annoyed- unless wizarding culture is very different for some reason, she should at least have been trying to restrain herself. 3- Part of the point of the fic was to attempt to popularise rationality (and it has at least extended the audience for Less Wrong's ideas). Given the necessity of that, changing Harry's backstory was probably the best way to do it.