This is the sort of thing that makes me appreciate the writing of New Vegas more and more, they take into account properly if you kill off 'main characters' you don't like instead of punish you for it, little to no RPGs do that these days. You can go on a massacre and kill everybody in game and there will be endings for that.
I was actually enjoying being a space pirate until i gunned down some guy for sassin' me which caused around 15 others to attack.
Imagine my surprise when every fucking one of them just stood back up after the fight.
I realize you can't kill story characters but almost all were guards or random citizens.
I kind of lost interest after that.
This is the sort of thing that makes me appreciate the writing of New Vegas more and more, they take into account properly if you kill off 'main characters' you don't like instead of punish you for it, little to no RPGs do that these days. You can go on a massacre and kill everybody in game and there will be endings for that.
It seems you ran afoul of the literal "protected" class.