I think the two versions of the story can be compatible. The 6000 years are just an information that was given by the computer and the people on the planet had to believe.
The main difference in the comic is that the crew of the enterprise met a person who has never been under Landrus influence and was able to tell the true story.
It's absolutly possible that in the Prime Universe the team that stayed on the planet after Landrus destruction found out the truth too.
P.S.: Please excuse my bad English. English is not my native language.