The mana progression really took me by surprise and while I understand the goal I feel like it has moved too far. As it stands it will drive conquest, but I feel like you can still achieve that goal, without entirely removing alternate sources.
There have been a lot of suggestions and a lot of response, because it cuts down on your freedom of action. Anyway, I was thinking of a couple things. You could have a altar, or statue, or magic circle, where the you might be able to put Shamans or other minions to allow for a slow trickle of Mana. Good for early game when you would like to progress some research. The idea of gaining mana by torturing and killing prisoner (dark though that maybe, haha) is a really good idea too. Sacrificing gold, sacrificing items, sacrificing minions, burning dead bodies could all easily give differing levels of mana based on the difficulty of action. Make like an old school Diablo II effigy out of body parts.
The change right now is good in the way that drives action. It leads to a more dynamic play style. I think the same goal can be achieved if the rate of return on attacking enemies is much higher than the slow trickle you would get from having a shaman pray. On top of everything though, sacrificing prisoners on a dark altar is a pretty flippin sweet idea.
Best of luck with everything, love the game, whatever gripes I have are lost in jubilance that I finally get to play a dungeon keeper game that has very little BS.