Nice theory - but it assumes the balladist must have been thinking of an actual event. Otherwise the title "Barbara Allen's Cruelty" seems to make no sense at all.

I don't think the ballads are much interested in medical diagnoses. Jemmy could have been dying of many things - including consumption or (at least in popular imagination) a broken heart. He says the basin is full of his "heart's blood," which at least allows that interpretation.

Also, if there was no prior relationship between the presumed lovers, why would she go to him at all - especially if she thought he might have the plague? And why would she want to be buried by him?

The conjunction of the possible appearance of the song at the same time as that of the plague might have given it added poignancy at the time, however.