Once you've completed the Blind Betrayal quest by saving Paladin Danse he is exiled from the Brotherhood, but he is still available as a companion. Under these conditions, asking Paladin Danse to accompany you will prompt a warning that while he is travelling with you both of you will be considered enemies of the Brotherhood. Any Brotherhood of Steel members that you come across will be kill-on-sight.
Now, obviously, fast-travelling to the Prydwen and stopping by Maxson's quarters to say hello would cause some real issues. But what about the random-spawned Knights and Vertibirds that you'll encounter in the wasteland?
Are there any long-term ramifications to killing randomly-spawned Brotherhood members while you are with Paladin Danse? Will killing these enemies hurt your relationship with the Brotherhood once you're no longer travelling with Danse?
Best Answer
I've played the game long enough to know that after the quest Blind Betrayal, you can attack any unnamed brotherhood of steel member with no ramifications. If you complete the quest and then side with any other faction that causes the Prydwen to be destroyed he will ignore you. So, you can do what you want with Danse as long as you don't go on the airship.