I wouldn't blame anyone for changing the 'and the train done gone' line.
People keep coming and .....?
I have a feeling that you are right and the first version would have something else (regardless of when it was first sung).

Johnson and Johnson, 1926, II, pp. 124-125 have the title as "Mary Had a Baby, Yes, Lord."

1.
Mary had a baby,
Yes, Lord!
Mary had a baby,
Yes, my Lord!
Mary had a baby,
Yes, Lord!
De people keep a comin' an' de train done gone.
2.
What did she name Him?
Yes, Lord!
What did she name Him?
Yes, my Lord!
What did she name him?
Yes, Lord!
De people keep a comin,....
3.
She name Him King Jesus ...
4.
She name him Mighty Couns'lor ...
5.
Oh, where was He born? ...
6.
Oh, born in a manger ...

Take out the last line, or finish with a line in keeping with the other lines in the verses. ??

The form suggests to me that the train line is a late add-on.