It's probably like everything else that started off with the best intentions. I imagine there were a few widespread vaccinations that actually worked (like smallpox mentioned earlier, though it's debatable of course) and for which the benefits far outweighed the risks, with unadulterated data to back it up.
Then the big dollars started flowing, the scientists and doctors became businessmen, "do no harm" started applying to their bank accounts instead of their patients, and it all went to hell.
I don't think the very first vaccine was some luciferian pharmakeia kabbalah conspiracy, but I also wouldn't be surprised if it was.