The conflict of The Chrysalids is very similar to the central conflict of many "post-apocalyptic" or futuristic works--man versus society. David, more than any other characters, represents this conflict. He knows that he is supposed to abide by the very strict rules of his society and live in fear of judgemental God exacting another tribulation about his people. However, his innate curiosity makes it difficult to do either. He befriends Sophie, who is not "normal" and who hides the fact that she has six toes. Anything considered abnormal to David's society deserves a banishment of sorts.
With a central conflict such as Chrysalids, a lone hero is normally forced to make a choice between all that he has known and been encouraged to believe/do and what his conscience, brain, or desire tell him to do. Other examples of this specific type of conflict include, Huck Finn, The Crucible, The Scarlet Letter, and Fahrenheit 451. The conflict seems to be applied most often to religious societies.