I'm pretty sure the first verse is about the inquisition and witch hunts, not the war, since this is more an anti-catholic song, and the pope was antiwar, so that wouldn't really fit the song.
"Innocence Burned, Alive on the Stake" obviously refers to the witch burning, in my opinion.
"Tortured and Dumped in nameless graves" is more related to the inquisiton, I think.
I'm pretty sure the first verse is about the inquisition and witch hunts, not the war, since this is more an anti-catholic song, and the pope was antiwar, so that wouldn't really fit the song.
"Innocence Burned, Alive on the Stake" obviously refers to the witch burning, in my opinion. "Tortured and Dumped in nameless graves" is more related to the inquisiton, I think.