Another guess at origin in "The Joan Baez Songbook," Amsco (1964, 1989): "...this song had to travel to foreign lands and be brought back to us before it achieved its rightful place in our songlore. It started as a Negro gospel song, "Come By Here, Lord," was exported to the West Indies where it was rephrased in 'pidgin-English' as 'Kumbaya,' and returned to the United States where it is now a great favorite..." Was Marvin V. Frey African-American? He wrote other religious songs that may be found via Google.
"Joan Baez Songbook," pp. 130-131 with music and chords.

Marvin Frey, composer of 'Kum Ba Ya' [Come By Here, Lord] died in 1992 of heart failure in North Tarrytown, NY. He had composed over 2000 songs of faith according to an article in Time Magazine.

Pete Seeger has a different story. "...in the Library of Congress they played a recording for me of that song sung in 1920. Marvin Frey made up the slow version about 1936-1937. He taught it to a family of missionaries that was going to Angola and there they changed 'come by here' to Kumbaya, the African pronunciation [Note- there are several linguistic groups in Angola and it is entirely possible that a 'pidgin' was used, possibly incorporating some Afrikaans words from the then Southwest Africa to the south]. Then it was brought back here." SEEGER
It is not clear whether Seeger is referring to the music or to the lyrics in what he heard at the Library of Congress. I can't find anything that seems like it in American Memory. Closest I can find is "Come Lord Jesus," by Root, but not likely.
Chorus: Come, come, Lord Jesus;
Born to set thy people free...'

It seems to me that the S. Af. story of Seeger's came later.