According to this thread: https://forums.beamdog.com/discussion/37145/not-an-issue-emmerich-died-in-werewolf-encounter
the issue of Emmerich appearing as a greater werewolf and attacking the party after all three of the trapper brothers had already been murdered (which apparently is a rather common occurrence, as it was in my game), and then him never having the opportunity to shapeshift back to a regular wolf and flee (thus preserving the ability to still save him and continue with his quest) is known and intended behavior.
I'm here to clear this up as a public service announcement and to let anyone else still struggling with this problem know that it's still possible to save him, albeit you're possibly going to witness a rather strange glitch while doing so.
In my game, as I mentioned, I came back into town after all three of the brothers had already been murdered. This left the gravedigger hanging out at the small graveyard with no real info other than all three were dead, and a state with Emmerich such that you can't talk to him about his condition and therefore appearing to have no way to finish the quest to cure him. The innkeeper is of no use, either. But here's the trick to kickstarting the quest back into working order again:
- If it's not already nighttime, rest in order to advance the time of day to night.
- As soon as you exit the inn, Emmerich (now a werewolf) will attack the party. DO NOT KILL HIM.
- In fact, all you needed to advance the quest was simply to have witnessed him as a werewolf and that he attacked you. IMMEDIATELY re-enter the inn. Rest again.
- Once daylight, exit the inn. You might notice (depending on the nature and frequency of the glitch), even though it's day time, Emmerich is still in werewolf form, but now, strangely, he's fleeing the party. He will not attack you now that it's day time. Instead, if you follow him, he'll retreat to the northeast corner of the map and just glitch there, endlessly, apparently attempting to enter the forest.
- Even though Emmerich the werewolf is still on the map, ignore him and walk down to his cabin. Enter and speak to him (huh?). That's right, he somehow teleported into his cabin even though you just saw him!
- Now you'll finally have the option to mention to him that you just saw a werewolf. You can continue the quest to cure him (or kill him) normally.
If you don't get back to the inn when Emmerich first attacks you at night, even if you attempt to restrain yourself and not kill him, it's simply not possible to progress in the quest that way. Even if you take him down to 1HP he won't submit or flee. If you kill him, his mortal body collapses and you've just locked out the ability to complete the quest, and, much more importantly, he'll never be able to sell you any missile ammunition again -- being dead and all. Trying to get through the rest of the game if you're low on ammo and nowhere to buy it aside from him can be a real pain.
I hope this info helps someone out there and clears up any remaining confusion about the issue.