Lloyd, in the liner notes to the Waterson's cd, says clapbooks of the 1840s helped the song to survive.
The Kingston trio site goes so far as to say Jesus was age 11, and that the story is an oriental legend known in Europe before the 11th Century. No references, of course! A likely story! Trivia courtesy Google.
Although suggestive of gnosticism, I doubt that there is any evidence of the song that far back. The Gnostics were pretty well wiped out by the Church, which did a better job of rooting out heretics and unbelievers that the Romans did with the Christians.