It's well past by this point, but Discord can be both evil and not truly malevolent. What he does hurts ponies, and there's no getting around that. That's bad. But he's doing it not out of spite or malice, but simply because it's what
he enjoys. He's not malevolent, simply selfish. He can still be, and indeed is, completely evil through all that.
As for the issue of him going out of his way to mind-rape the girls, well, that's pretty chaotic. He wanted things to be different, and disliked that fluttershy refused to change for him. Pretty simple chaos, there.
I'm not going to touch the issue of flaws myself, save for saying that yes, it's good that they all have flaws, but that still doesn't mean we have to like them. It's perfectly natural to want to see someone overcome their flaws, or at least dislike them for those flaws.
edited 17th Jan '12 12:31:56 AM by kegisak