Sagan does not say that there are 'undisputed truths'. He says that if something pretends to explain something that is already explained in other ways, than the explanation has to be better.

This is exactly what happened with virus and bacteria. The concept wasn't known, but if true, it would explain what was known AND it would answer other questions too. It would be a better explanation. Then it became a question of experimentation to see if this theory could be tested and if the experiments would deliver better results than those based on the previous concepts. In fact the theories of bacteria and viruses explain the transmission of disease better and the greatest medical discovery of all time, the washing of hands, was the result.

What Sagan says comes down to giving us a measure whereby we would not go back to believing that prayer is more effective than washing hands. All this doesn't mean that in future there are no new discoveries that improve our understanding of diseases and their transmission methods.