I lived through that, and being a once-and-former D&D and Traveler role-player I had the inside knowledge of how the accusations were more fictional than the game. While it's true that the players I knew were more often than not non-Christians and agnostic or atheist, they more certainly weren't atheist.
That entire episode was a scheme to "Other" and create scapegoats out of an atypical class of people. The people who concocted the scheme were looking for more "witches" to burn to distract from other issues. That should sound very familiar.