so i threw a Grenade and it accidentally killed some ncr dude and they all start shooting my [censored] so i kill like 3 of them. then every time i see them now they shoot me??? how do i get back in their good books?

kill more, take armor, and do some quests.

Crap happens.Go work for the legion.and be careful not to blow them up...
All else fails? kill em all.

Once they are attacking on site...your pretty much hosed.But there are other options.
So yea...live and learn that killing folks comes with a price.

Your decisions actually matter here. I wish the story would veer off into caesars legion since I'm pretty much sided with them by spreading the word. Still early in tge game though...