I don't know about scrub as it doesn't alter version history but user data such as passwords, IP addresses, etc.; but to shun an artifact definitely meets my criteria for falsifying history and thus lying. I neither suffer from cognitive dissonance nor feel the need to defend a piece of software's honour.
What negative language? You seem to be attributing your own negative connotations to a word that is being used descriptively—not disparagingly. And the shun page explains that you should not be removing content willy nilly but only as a last resort to, for example, remove sensitive information from the blockchain. The Fossil authors are perpetually behoving users not to use shun unless it's absolutely necessary, but provide the feature as a necessity in case someone foolishly commits sensitive information that could land them in legal trouble.
Would it make you feel better if there was a note on the page that said "NOTE: By using this command you will be lying about the history of the repository and should document the removal explaining why the artifact was excised from history." Submit a patch. Improve it.
So... there's both shun and scrub in Fossil, which lie about project history? Or is is not accurate to call it lying in this case?