I resurrected him and used him for a bit, then fired him back to Novac. I came back for him a few days later and he was dead in the same place. There can't possibly be any hostile creature killing him since Manny, nor anyone else in Novac, ever gets dies. If I dismiss him to the Lucky 38 he will remain fine.
I never receive a message saying that Boone has died and he's always in the same location under Dinky when I find him.
Is he scripted to somehow kill himself if you leave him in Novac too long or is this some kind of bug? If it's scripted, I certainly wouldn't expect this to happen after finishing his quest.
I've also asked over at http://www.newvegasnexus.com/downloads/file.php?id=44204's mod page.