So here is the scenario Im looking for an answer to. Ive restarted a new game, played all the way through up until the point where I go kill Benny. What I plan to do now is go do LR. I would like to Nuke both the NCR and Caesar for the loot, then go directly to the Tops and kill Benny. Then when I leave the Tops is when the NCR and Caesars guy run up to me and tell me Caesar and NCR have forgiven all my past sins, and please come see them. If I do this, will it prevent NCR and Caesar assassins from attacking me randomly in the future?
No idea, but you could always make a save right at the end of LSR, bomb them both, go deal with Benny, get the forgiveness from CL and NCR then walk about for a while and see if you get any hit squads after you.