I love my characters, so even when the evil ones want to do their own thing, I can't do anything but shrug and sigh and rant about it to my other characters. The thing about characters, I've found, is that they tend to stick together. When they're doing what they want, they may hate each other, but let me try to control the story and BAM! You've got the prejudiced girl and muggleborn bound together in their resistance. It's rather cute, sometimes.
Maybe that's why Lily stopped hating James! Jo tried to change the story, and they decided to band together to keep the story the way they wanted, and Lily fell for James!
But seriously, I think you just have to let go of your characters for a bit. After all, they tend to know themselves better than you do.