In trinity I agree the deliverance engine was a joke, and quite frankly it's pretty pathetic conpared to the novalith or the kostura. That said, it's usefulness has gone up somewhat with the new advent bonuses in culture.
However, I think the biggest problem with it right now is theres an easy counter to negate most if not all of it's effects. I got shot 3 times by one yesterday and because of the sheer number of culture centers I had, their cluture didn't even register on any of my planets that got hit. No allegiance change in the slightest and no reduction in culture output. After the third shot the AI scuttled it.
On the other hand, I don't really see a defense against the kostura. The novalith, the obvious defense is to get aux. government, which depending on the size of your empire, that's a lot of starbases and a lot of resources and even so, it will still kill population reducing tax income, and reduce your trade income. Against the deliverance engine, just add a few culture centers and I think the only buff they will get from it is the damage bonus.