An article from Online Athens reveals that Mary, the sister in Laura Ingalls Wilder's "Little House" books, was probably blind due to a fairly common disease, not scarlet fever.
Based on Wilder's letters, unpublished memoir, historical documents and biographical record, Mary probably had a viral form of meningoencephalitis. This disease, though easily treatable today, can cause fevers, headaches and seizures. It can also lead to blindness if it affects the optic nerve.
There is a similar story based on the young women in "The Crucible". Rather than actually having hallucinations and seizures due to witchcraft, Linda Caporeal discovered strong evidence that the girls were actually suffering from Ergot poisoning.
Ergot is a fungus sometimes found in rye, which was a common, cheaper replacement for wheat in the 17th century. Ergot contains a major component of LSD, lysergic acid, which would explain the symptoms the young women were experiencing. They were more susceptible to the ergot poisoning because of their small stature.
Do you know any other examples of literature that have been disproven or brought to light by modern science?