...do note that Hermione at one point reacts in a genre-savvy fashion by saying that it's fine for Harry to have a dark side.

Please keep in mind that a lot of this apparent problem is generated by the unalterable fact that Harry, who has Stuff Going On and has been through hell as the title character and has to grow fast enough to be competitive with people like Dumbledore and Professor Quirrell (all genders chosen by Rowling) happens to be male, whereas Hermione, who like many other characters is going to have difficulty competing with Harry at this point in the story, happens to be female. I mean, suppose Rowling had made her professionally paranoid Auror a woman. It's not unthinkable that someone might complain about how Harry, a male, managed to land a stun on Madam Moody. Symmetrically, if Draco had discovered Harry doing science with Hermione some chapters earlier, he wouldn't have had the same reaction but he would've had an equally difficult reaction for Harry to deal with, and yes I would've figured out some way to make the adultery joke there too.

The main lesson I'm learning is that there are potential Problems when you arrange the plot so that you have the main character interacting with two different tiers of powered characters (Harry-Draco-Hermione and Harry-Dumbledore-Quirrell) and you haven't arranged the plot to have the main character's companions go through everything the main character does... but that problem is far too late to correct now.

P.S: In retrospect there's exactly one important canon character in this story whose gender I could freely choose, and I did happen to make her female, but that's not going to be apparent until later.