When you get the option to punish or absolve, select the absolve option. After a while once the metre fills up, you will level up your holy skill. Small demons are worth 10 holy points, larger demons are 100, and the shades also give you a lot, so if your going for the holy path, make sure you absolve them.
Edit: m0rph3us17 brought up a good point, there is an accessory that lets you get 30% more holy points, Im not sure if this is a story related accessory, I can only remember that Minos Tail gave you 30% unholy from King Minos. There is an accessory guide on here though, so you can check that out.
Credit to rastal66 for mentioning Charons Oar and where to find it:
-*****Charon's Oar****** : When hanging on the side of the ship, do not go up into the ship, hop further to the right to find a demon dog in an alcove.