I don't think it is. 'Pale Blue Eyes' seems to be more of a work of artistic expression than a retelling of actual events. Songwriters often draw from various inspirations to craft their compositions, not necessarily from true stories.
Pale Blue Eyes is not based on a true story. It's likely the product of the author's imagination or a fictional concept developed for artistic purposes.
The characters' relationships could be one of the elements based on the true story. Their interactions, like the way they suspect or trust each other, might have been modeled after real people's relationships in the true story. Also, the main mystery that drives the plot could be rooted in a real - life mystery from the story it is based on.