Storyline Quest and Tavern Quest are two separated quest and don't affect each other. I finished the Farolin storyline quest without doing it's tavern quest with no problems.
The tavern quest doesn't have final quest and you might be given same quest over and over (as long as you're still on the same tier).
PS: You can take both quest that have same killing objective and finish them in one go. Just like "killing two birds with one stone". It Doesn't work with gathering resources/crafting missions though.
