in my first run through, I had only gone to the railroad for the courser chip, so I didn't have too big of a tie with them, but I did feel really shitting having to go in and kill them all. Also in my first run through, my charisma was not high enough to convince Danse to live, so I felt absolutely horrible after having to kill him.I felt kind of bad running in and slaughtering the Railroad, and seeing my codename on their blackboard and stuff, but then I remembered liberty prime so it was all ok