Finally finished the betrayals quest with the help of guild members. I am once again able to go into a city. I got an apartment just fine but don't seem to be able to go into any of the craft guilds. The guide I followed did not mention leaving your craft guild before beginning the quest so I may not have done this.
I haven't poked around all the craft guilds yet though. I believe there is only one in Willow Wood and that is where my apartment is. Does anyone have any suggestion son this?
BTW. I think that the entire quest was a lot of fun allthough you certainly do a lot of running back and forth at the end. But in the end all my sins were forgiven and I am accepted into the city. Woohoo!