So as part of the Crimson Caravan quests, I picked up Cass, who gave me her own quest. During the course of her quest, I started to work for the Van Graff's for easier access to their headquarters. Now I've finished Heartache, peacefully, giving the Evidence to Ranger Jackson, and he specifically informed me not to kill Gloria Van Graff or Alice McLafferty. However, I still have the Birds of a Feather quest open. Now I know that if I bring her there I get an option to tell him to he'll be sorry if he shoots her, but then I have to kill everyone in The Silver Rush. Will this cause me to lose fame with the NCR? Or because I've presented evidence to them will they know they are murderers and it wont matter?

Pretty sure going genocidal on the Van Graff's doesn't hurt any reputation other than with the Van Graff's specifically. its the Crimson Caravan that you don't wanna mess with. They are NCR, AND the Strip.

Might I advise you, if you are going to have to kill the Van Graff's anyway (If you want to keep Cass, and why wouldn't you?!) then first, go do the Hidden Valley quests, and get up to the part where you are asked to eliminate the Van Graffs anyway. Two birds with one stone, etc.