This quest has you kill the emperor via any means you wish however the quest guidelines suggest via the gourmet chef way, but poisoning the soup and then having him eat it. While this method may seem tedius and unnecessary vs's just killing him yourself somehow.... Understandably it's a poor attempt to follow the rules of the brotherhood to remain concealed and unnoticed. Very poor one... it just..... doesn't make sense honestly...
Specially considering all the difficulties spent trying to ensure there are no loose ends.... if anything should be forced to kill the chefs assistant followed by killing the emperor followed by anyone else that may have seen you during the normal routine...but anyways....
That's besides the point i'm trying to make however.
The point i want to raise is this glitch that occurs.... Alternatively to kill someone without being hit with bounty or being recognized would become a werewolf. Provided you do this out of sight, there should be no issues.
However if you proceed to enter the area, avoid the chef part, and ensure your not being watched/seen, change into a werewolf and go storm in on the "emperor" and kill him. The dialogue that follows messes up, your still hit with a bounty..... things just "go wrong".. it's as if the creators of this quest wanted to make certain that you could never finish the quest without a bounty in solitude. Bad design i would say. I slaughtered everyone in the emperors dinning room and slaughtered everyone around that tower on my way to escape the town without being hit with bounty... but it's hard coded not to allow such.
Among all the quests that need fixing.... i don't beleive this is super critical at all, but i do beleive it should have at least a little attention.
at least a temporary alternative would be to add a console command that removes lifetime total bounty instead of only the specific town bounty.