Willie Pappas

I found you can run past the guards and hide until agro calms down. This will, at least, let you finish most of the missions, like the peace talks. It's easier to do if you don't have companions with you. Also, you have to fast travel to the back end of the ship

I have also run into this same issue and it's preventing me from completing a number of quest. I'm trying to wait the 3 days but as I'm not sure of how long this takes, real world time, I am not sure if this is just broken or if I have not waited long enough.