It IS about cannabalism!
From what I've read about the writing of the song, the writer got his inspiration from a book on late 1800's mining. One of the pictures in the book showed a team of men working with a small donkey/mule in the mineshaft, and the caption read something along the lines of "mining crew working with Timothy at the [whatever] Mine."
So the writer wrote the song with two miners, Joe and the person from whose viewpoint the song was written, and the mine-mule Timothy, leaving it purposely vague so as to infer that Timothy was actually another person.
That may or may not be apocryphal, but, anyway, that's what I read about it ... and I know that Wikipedia says something different ...