If you look this song up on the Annotated Grateful Dead website, by David Dodd he says
"He's Gone as originally 'written, referred to the disappearance of Mickey Hart's father, Lenny Hart, who was acting as the band's manager, with a good deal of money. (See interview in Relix, vol. 5, #2, p. 24.) Since then, the song has become riddled with meaning, played often quite tenderly when someone close to the band dies. "
If you look this song up on the Annotated Grateful Dead website, by David Dodd he says
http://arts.ucsc.edu/gdead/agdl/gone.html