First of all, I enjoyed this story, it many ways it was very classic sci-fi, its takes an idea or concern and either presents it from a different point of view or takes it to an extreme and I believe this story did both.
The conversion from a Christianity that follows the Bible, to one that follows maps is fascinating. As well as that there were different "local" ,kinds of Jesus, this reminds me of a discussion in a college class about the different forms God used in the bible, where you see Yahweh and Elohim, the latter I believe carried the connotation of a Deity which you had more a personal relationship with, please check on it yourself though I am by far not an expert. This is also reminded me the Hindu religion and in tangent the Shinto religion where there were often spirits for everything and everything had a spirit, respectively. Not to mention the legion patron saints to be found at least in Catholicism. Which leads me to believe that because of such different visions the truth came to be identified with different objects, to maps for the cartographers, perhaps to DNA for the biologists? Though it is hard to imagine the sort of technology surviving into this world.
I didn't notice any hints as to what had happened that caused the unusual mixture of technologies that would leave a diesel bus, expensive but sounding common and then oil soaked paper as the method of transporting fragile goods. Though obviously this wasn't the main piece to the story. We were also not quite told what the non-religious people of the lake actually had for technology, they were in mud huts, but our group we followed wasn't exactly living the high life either.
Yet there intention was to literally, move mountains. I recall the comment on the mustard seed myself, though I was never raised on the literal Bible position. Which makes their actions all the more intriguing and recalls, the Calvinists I believe, who understood that success in life showed that you were one of the chosen, such that working hard and succeeding was a back-door way or ensuring your place in heaven. And it could just as easily be that none of these influences were meant to be applied as none of them.
At the same time I'm struck by similarities between this group and some of the Green movements, the need to keep land natural and the way it is, small parts willing to even resort to terrorism to stop what they see as evil, similar as well to the Red movement of the Mars Trilogy, in their effort to keep the primeval, the correct, the true Mars, alive, well, red.
In contrast to others though I believe that you could had substituted any fundamentalist group into this story, that a group of rogue cartographers trying to return the ideal that their maps of old represent would have worked fine. I can only assume the author intended to raise some of the ideas and question that come from the change a religion will go through as it moves through time. So the question of why Christianity was chosen is invariably raised, and this obviously got a reaction out of people. I am not familiar with the author so I wouldn't be in any position to suggest why.
Overall I enjoyed the story, I found it thought provoking on quite a few levels and hope this gets suggested for a Hugo in the years to come.