I would love to kill them but I love Whiterun lol. The reason why they are attacking me is because on the quest, where I need to kill the Emporer III, The emporer asks me to do a favour before I kill him, which is to kill the one ordered to kill the Emporer, makes sense? So I killed him, but, I even closed the door, and nobody was in it except him.
But It's fine now, I loaded back right before I killed him as I remember I made a save just to make sure.. And now after I killed him, I was able to clear my bounty.
But when I'm done with the game, I'm going to go to each and every city and kill everyone.. Do they respawn? If I travel to Whiterun and kill everyone there, and then travel to a different and travel back, they will all be dead right?