Hi, Joe -
for the sake of discussion, I added the lyrics from the link to your post. The best darn book about Pete Seeger songs is his Where Have All the Flowers Gone? - A Singer's Stories, Songs, Seeds, & Robberies (edited by Peter Blood Sing Out! - 1993). Here's what Pete says about the song:

Some parts of the world (Japan is one) like songs in a minor mode. Some individuals also. Most of us now go back and forth easily - too easily? - from one mode to another. The next song, like the last two (I Have a Rendezvous With Death and The Torn Flag), is in a minor key.
The weakness of any allegory, here, or in the Bible or anywhere, is that it can be too pat. The "meaning" of a work of art should shift, change, expand. However, this allegory worked. I've had requests for it 20 years later. Today the "eggheads" are warning us about the oxone (sic) layer, global warming, overpopulation, etc.

Most of the time, the book gives wonderful background stories for songs, but I have to say that this is one time when Pete's explanation of a song is a bit cryptic. Since he says it's an "allegory," I would suppose it's fictional - but maybe not necessarily so.
Interesting question, although I can't say this is one of my favorite Pete Seeger songs.

-Joe Offer-