I believe it is intended. Religious units travel in a different "plane" than military & civilian units, which is why they can occupy the same tile as such, including such enemy units. So I'm not surprised that a tribal village occupies the same "plane" as military & civilian units, and religious units just pass through them.
While religious units can occupy the same tile as an enemy unit, e.g. a barbarian, even barbarians can still condemn them as heretics.
Monks are the exception, as they behave as military units, although they count as religious units for the World Congress Resolution on World Religion.