> plague doctors who made efforts to protect themselves.
Indeed - the figure of Il Dottore from the Commedia Del Arte wears a mask with a long "beak". The beak was stuffed with sweet-smelling herbs; in those days, they thought that it was bad smells that spread disease.
Perhaps people gathered in churches because they burned sweet-smelling incence in churches?
People knew there was something going on between infections that spread them even before the more advanced germ theories of Pasteur.