I think "these worthless beings" could be referring to the four playable characters in Shadows of Evil. In Shadows of Evil's cinematic prologue, the Shadow Man says(speaking to the playable characters), "why do you do the things you do? Do you not see the futility of your tiny, insignificant existence? You are but fragments of a bigger universe." The Shadow Man seems to believe they are worthless beings.
If this note was in fact created by Maxis, maybe he was communicating with the Shadow Man asking him not to eliminate the "worthless beings," so he can utilize them for God knows what.