If you killed Nathaniel without asking him who is behind the attacks and murders, then you really missed your chance to fight Hubert. You can kill Nathaniel after learning the info about Hubert but don't kill him the moment you see him torturing the girl in the bar.
Haha, I missed it too. Then I heard a spoilercast by The 40 Cast and realized what I did. Luckily I am playing through again anyway and I remedied it. I was so mad. I jumped the gun too. Sorry man, but glad I'm not totally alone on that one.
