Then you shouldn't have shot their leader. Really, what did you think was going to happen? "Hey, you just shot our Father, the leader of the Institute and the one who was going to usher us into a new era of prosperity? Don't worry, we're cool. Enjoy your visit to the Institute! Now if you excuse me, I have to mop up his blood and arrange for his burial."

Lesson learned: if you intend to start a fight, be sure you're well equipped for it. Either try to fight your way out of it or reload a previous save.