Well, I met Benny, didn't attack him right away, went with him up to the Presidential Suite, and basically said I would think about whether to kill him or not. Then I was approached by the Legion's emissary, went to the Fort, and there was Benny! Then I completed the blowing the reactors up quest for Caesar, and had him crucified. However, the Wild Card quest continued open, so I figured it was worthy having a second look at the Suite, since I had the keys and all.
Hence I was more than surprised when I entered the room and there he was, Benny, alive and having a drink on the counter! Is there a way to fix this? Some sort of console command or something? It annoys me a great deal.