I think the prison is fine as it is. Maybe a little bit grindy, but overall I had a lot of fun, just exploring and figuring things out. And if it's not broken, don't fix it.
A tally might actually be redundant. Given the difficulty curve, clearing the prison without holy items kind of necessitates getting everything you can. And if you take holy items, well, there are already some punishments in place for this, namely missing out the only two items you'll get to keep when outside.