I'm beginning to think that there may be no such Baptist hymn called "Lay the Lily Low" and some folklorist back in the day got their wires crossed and somehow conflated the Jack Munroe ballad with a supposed hymn. In this 1978 recording, Florence Reece talks about getting the tune for the song from "I'm Going to Land on That Shore"- many versions of which are still sung today.
Listen here: https://dla.acaweb.org/digital/collection/Warren/id/2200/