Just because on popular pseudo-scientific theory was successfully debunked doesn't imply that all theories can be debunked. Arguing with the vaccination case here boggles my mind, it's so misguided.
Correlation doesn't imply causation, but causation DOES lead to correlation obviously.... and the reason those vaccines are done, idealistically, is because they've been proven to work. Epidemics of non-vaccinated people wiped out entire cultures.... The only reason we don't hand out smallpox vaccines is because it's considered by health authorities around the world to be eradicated..... the last known naturally-occurring case was in 1978. At that point, vaccination is more dangerous that not vaccinating - but if smallpox were to arise again, you want to vaccinate as many people as possible to protect everyone.