ShadowWulfe: I removed the maps from the save files. The maps were reset, but the lycanthropy quest was not.
Did you try actually copying virgin map files into your save folder? It may be that simply deleting the maps doesn't reset them properly. Just guessing here.
I played with Xolotl's editor for a bit, but saw nothing to edit quests. I was able to get a script editor for the hunter, but it didn't actually let me see or edit the scripts, just rearrange their order.
I'll add that I don't think you necessarily have to attack the merchant without provocation, you just have to have the quest still active. I'm guessing what happened is this:
Talk to hunter. Get Lycan quest 1 (kill merchant).
If you talk to the merchant and agree to kill the hunter, the "real" lycan, then at that point Lycan quest 1 = FAILED. You then have Lycan quest 2 appear in log (kill hunter). If after getting Lycan quest 2 you THEN kill the merchant and take the pelt to the hunter, the hunter won't care because Lycan quest 1 is already failed. If you right click your quest book, you'll see a list of all your inactive quests. Lycan 1 will be there.
Other than this, I'm sorry, I don't know of anything else to suggest. You could try asking the dev (Basilisk Wrangler) or other posters on the official forum, but I doubt you'll get anywhere. It is an indie game after all, so everything isn't polished nicely.
At the least, if you kill the hunter now you can take his ring, which offers a minor magical bonus. You'll get a few coins for selling it and killing him may remove the lycan quest from your log.