Basically, yes. Lenny died in August of '66, and this recording (October 22, 1966) is maybe the song's first public performance. Phil pulled a table on stage so he could cheat and have the lyrics in front of him it was so new. In the same concert, he dedicated "Pleasures of the Harbor" to the memory of Bruce. Obviously, this song ends in suicide, whereas Lenny died of an accidental overdose. I think it's likely Phil wanted to write about Bruce and instead it morphed into this song.
Back in 2019, I had dinner at the home of Leni Ashmore Sorenson, formerly of “The Womenfolk”. She, like Phil, was part of the Greenwich Village folkie scene in the early ‘60’s, and she told us that she sublet her apartment there to Phil when she moved out west. People kept stopping by asking where Leni was, and that, she said, was what was behind the refrain of this song.