Premise: There is a deliberate agency managing an elaborate reward/punishment system according to its own standards for behavior.

When the travel of news through a community is slow, and its travel across communities nonexistent, a mystic class could maintain this story in the context of empirical reality without conflict. Did your neighbor lose a few head of cattle? It's because he upset the gods somehow. It's not even necessary that the subject of the story exist, since the flow of information is congested, and standards of plausibility indeterminate.

But as information begins to flow more readily, and natural and scientific precedents sculpt a culture's perception of reality, ideas that no longer appear to describe reality are more likely to be recognized as such. The dilemma then becomes how a mystic can reconcile his notions about the world -- of divine justice, etc. -- with a growing probabalistic model that is casting his view under suspicion.

Take the conflicting conceptual space the idea occupies, and posit it as an actual space. Better yet, make it a place from which you don't generally expect to hear reports back from.