"Religion is the greatest form of crowd control." -NapoleanI think this is right - I doubt that the average Imperial citizen has very accurate ideas about the boogieman, but he certainly thinks that there is a boogieman.
It's "just a story" in that the details are almost certainly wrong, and I'm sure there are things about Chaos that your average Imperial citizen hasn't even thought of. In fact, I'm not sure your average Imperial citizen even makes much of a distinction among Chaos, xenos, normal mutation, and plain old human heretics or apostates.
But it's not "just a story" in the sense that your average Imperial citizen thinks that the church's teachings about turning from the light of the Emperor are just complicated ways of getting people to behave correctly - as though he thinks, "When the Ministorum talks about mutation being a threat to immortal soul, it's really just trying to enforce a uniform code of social mores for the efficient governing of Mankind, and possibly to prop up its own decrepit power structure as well."
He thinks, "When the Ministorum talks about mutation being a threat to my immortal soul, it's telling me that mutation is a threat to my immortal soul."