Does the vaccine pass down throughout the generations?
If so than the Enclave becoming successful with their plan is the only way we would ever know (with the New Arroyo and people from their being the only ones to survive, along with the Enclave ofcourse).
The Enclave on the Rig and Navarro did not get the vaccine. They were working on it, just finished seeing as it works on the Chosen One and the Captives but it killed all the Enclave scietists/civilians.
The Enclave in Fallout 3 changed the curling virus again to make it water born, and more specific in who it targets.
Like most vaccines I would Imagine that I would be passed down to the young but would go away after a couple generations. Just like the smallpox vaccine. Then again we are dealing with SCIENCE! so it could very well be a multigenerational vaccine. It could have been more of a gene therapy.
So if the Enclave did somehow manage to do their plan again.. The people of New Arroyo could very well survive.