Hello!
I started looking for some information about this old song after watching the "Magdalene Sisters" film and I found your discussion, which is very interesting.
I am from Greece and I don't have some information about this old song, but I surprisingly realized that it reminds me much of a Greek folk song. This song is called Menousis and it is a story about a murder. Three friends were drinking and discussing about beautiful women and one of them insisted that he had met his friend's Menousis' young wife who was in the well to take some water. The man told his friends that he asked her to wash his towel with the well's water -asking a young woman for "a favor" was at least something like sexual harassment, especially a young married woman. He insisted that he knew her very well, that he knew what she was wearing under her clothes etc. In the end, the woman is being murdered by her drunk husband, because "she acted like a whore".
Also, I read about the symbolism, the well is a very common element in the folk songs of Europe, because it used to be the only place that the women were alone and so the men could come closer to them. Also,the lily is the flower of the virgins, so maybe it has a connection with the innocence of the young girl.