What is the main theme in "The Waters of Babylon"?

I would say that the theme of the story is the difference between knowledge and truth. The son longs to learn the secrets of the “dead places.” His journey to the bombed out city is forbidden by the laws of his people, but he is compelled to go nevertheless. What he discovers is that the “gods” of this place were not gods at all — they were humans like himself. While their technological achievements were very great, the “gods” were most definitely fallible, as the ruins of the great city attest. 

The son’s thirst to know is distinguished from the laws of the priesthood and of his society, which forbids travel to the dead places. The “truth” about these places, as he has learned it from his father, is that they are dangerous, poisonous places, and that the ways of the gods are an unsolvable mystery. These rules are in place in part to protect the hill people from making the same mistakes the “gods” made. As his father puts it after the son tells him what he has learned, “If you eat too much truth at once, you may die of the truth,” meaning that sometimes people are not ready to know everything. Although the son was compelled to break the law and visit the city to see things for himself, afterwards he comes to understand why the law existed in the first place — to prevent the people from “eating knowledge too fast.”

The story ends with the son deciding that once he becomes priest his people must return to the dead places to “rebuild.” The presumption is that their relearning of the old knowledge will be tempered by the truth that great knowledge does not make one infallible.