The long rule of the Myrkridia isn't a GURPS thing. In Myth: TFL, Balor's flavor says, "Second Era tradition tells of a hero rising in the East, who loosened the bloodless grip of the wicked things which had dominated his land for time beyond memory ... " While it doesn't specify a thousand years, the Myrkridia were around and running the place for a long time.
Also, humans weren't totally helpless. The Myrkridian Ghost text reads, "[Many of them] were slain when they attacked Muirthemne, and their cursed blood seeped into the ground... not every mysterious disappearance could be traced back to the Spider-cults." So the humans had some protection, at least in their walled cities.
