Why I think the Confessors wrath ability is somewhat less potent than other faith abilties
Wrath is also very easy to use and doesn't require any support from the rest of the SoB army. It is good for insta gibbing lightly armored enemies like fire warriors, guardsmen, reapers or scourges. Other abilities aren't so simple, they work in conjunction with an army. Emperors Touch is no good if the squad is likely to be tied up in melee. So you need good support atleast another 2 squads around the squad doing the Emperors Touch. Holy Edict rarely works from my experience (same bug as chains of torment etc - except worse in my experience). But when it does work, its useless if you don't have a heavy bolter mass to cut down the frozen squad.
To be perfectly honest I sympathize with the OP to an extent, because you very rarely see the T3/T4 faith abilities. I bet a lot of mid level players have never even seen one or more of them. Personally I might use avenging angels in a 4v4 if my team has more or less won and I have the luxury of building up holy icons and teching. But Divine Retribution...never see it. Avenging Angels...never see it in a tight game.
The main reason for this is that in a tight game you don't realistically have 5 LPs upgraded with holy icons. You are lucky to have that many points on a lot of maps, and regardless of how many points you have, in a close game, you are frequently losing/rebuilding Listening posts as parts of your base come under attack. Since the final Holy Icon is the most expensive to build, and is always the first to be destroyed, it is very risky to build all 5 holy icons in a close game. Typically I would get 3 holy icons so that I can use emperors touch, purifying light and the confessor abilities. And with a few faith producing units on the field, I rarely need more "faith store" then 60 to use those abilities, due to their recharge time.
Would I change anything? I wouldn't touch the faith cost of any abilities for the reasons outlined by others. But what I might change is the cost of the final 2 holy icons. It is currently too risky to build them in a close game because if any holy icon gets destroyed, the cost of replacing it will be equal to the cost of building the last one. I would suggest either:
How I would balance the faith system
-Cap the cost of the holy icons at the cost of the 3rd icon (you could reinsert that cost into the research of Divine Retribution and Avenging Angels)
-Leave the cost as is but make them free to rebuild if destroyed