What is John Wyndham saying about David's beliefs and values and how do they effect on his behavior in The Chrysalids?
Oddly enough, somehow David, even as a young boy, has values and beliefs that are different from those of his father, the Magistrate of Waknuk, and different from most people in his community. To make this difference believable, John Wyndham gives David an Uncle who sees for himself the error of the fanaticism of the belief system in Waknuk. Perhaps Uncle Axel saw enough of the world beyond Waknuk or understood and believed the reports of that world enough to give him a clearer vision and more reasoning attitude.
In any event, David's values and beliefs are innocent ones of inclusion and tolerance instead of blamable ones of exclusion, punishment, and division. The irony is that in the end the Sealanders turn the final judgment against the Waknukians who are demolished in death.
Wyndham's interest was in how long-established beliefs and values--logical systems--are detrimental to the survival and integrity of humanity when the world drastically changes, through one means or another. It was Wyndham's belief that logical systems had to be reframed in such an event, the way the Sealanders did--and the way David was doing. Of course, David was helped along by the fact that he had a Deviation that made him a Blasphemy and subject to punishment, even death.
David's values and beliefs led him to behave in a way that was loving and kind instead of punishing and coldly distant. He was led to help protect and guard instead of expose and harm. An illustration of this is the incident with Allan and Sophie. Allan was of a comparable age with David and, whereas David was gentle and kind with Sophie and quietly protecting her, Allan judged and condemned her and loudly exposed her resulting in her punishment and banishment.
Further, David's beliefs and values led him to lead, counsel (following Uncle Axel's admonitions) and protect the other telepaths in and near Waknuk, including his younger sister, Petra. Finally, he was led to summon the courage needed to lead the other telepaths in their escape from Waknuk, with his avenging father is hot pursuit.
When we meet David at the beginning of the book he is an innocent boy still trying to understand the world. While he has been taught Nicholson's Repentances and this community's interpretation of the Bible, he still has the innocent eyes of a child and sees a person's humanity despite his father's teachings. Even right after David meets Sophie, his childhood innocence (and in a sense, ignorance) allows him to mentally bypass Waknuk's teachings:
WATCH THOU FOR THE MUTANT! faced me as I went in, but it was much too familiar to stir a thought. What interested me exclusively at the moment was the smell of food.
Because of this, and perhaps because David has always known deep down that he too, is different in someway, he is more accepting of others.