That's what you get for wanting to murder innocent NPCs for their worldly possessions.
I don't even know what you can do to raise your reputation. It's very much a hidden part of IWD, as opposed to BG.
I don't know of any other way to get the bow, even if you manage to kill Emmerich "legitimately" while he's a werewolf (by stunning and killing him, or handing out so much damage he doesn't have a chance to run away. The bow doesn't show up anywhere if you kill him in werewolf form.