Actually, there are some misconceptions about the inquisition. Most trials were not set to confirm witch accusations, but to refute them. Several popes actively acted against popular witch beliefs. The focus of the inquisition was on heretics, not witches. This shows that the religious discourse was well aware of the distinction between exaggerated hysterical folk stories and ‘true’ supernatural powers.
Please check again where exactly we find Mara as a real being in the suttas. I recommend focusing on the SN and AN. You’ll see that Mara as a being is mostly limited to SN 4 and SN 5 - apart from that only in SN 2.30, SN 35.240, SN 51.10 (AN 8.70), AN 2.282, AN 4.15, AN 9.39.
So, basically Mara as character who acts, speaks, and thinks is a feature of SN 4 and SN 5. This can hardly represent early Buddhism in its entirety but is obviously a specific transmission line of a fable-prone transmittor, not unlike SN 11 regarding Sakka. The texts themselves treat the several Mara images as mutually exclusive. We find neatly separated Mara-as-khandhas in SN 23, and Mara-as-salayatanas in SN 35.65.