You can get this ending by murdering characters. The game locks you out of loads of areas after your first, so you might as well take the opportunity to kill everyone on your way and also get:
These are the poor saps I cut down:
- Cripple using oars as crutches
- The nude bowman up by the guy being roasted over the fire
- Man tied to tree (with apple on his head)
- The poor chap being roasted over the fire
- The ‘dead’ (sleeping) guy in the graveyard
- The gatekeeper with the massive key
- The Ferryman
- The two scholars inside the Basilica
- One of the cardinals inside the Basilica
Then try to kill Heavenly Peter. Once you're back in control, 'talk' to the crucified fella a few times to complete the game.
benveg (in comments) and
JayDiggler (other solution) both point out there's a second way to do this:
*** Spoiler - click to reveal *** When you get to the end and see Heavenly Peter, slap him three times and he'll call the guards on you. Then you'll be crucified and keep clicking on the nails to scream until the achievement unlocks.