How does Wyndham show that David’s father’s beliefs are wrong in The Chrysalids?

Wyndham shows that David’s father’s beliefs are wrong because he is abusive toward his son in the name of religious zealotry, and victimizes innocent children, even babies, because they somehow do not fit his narrow view of the world.

One of the ways that Wyndham demonstrates how ludicrous David’s father’s beliefs are is through the incident with Sophie.  Sophie was a girl with some extra toes.  This does not make her dangerous.  Yet according to the gospel of Joseph Strorm, it makes her an abomination.  Sophie has to hide, and is in fact caught and sterilized, then ostracized to the Fringes.  If this treatment of David’s friend were not bad enough, David’s father also tries to whip him, and does savagely beat him, even though he is just a child.

David demonstrates more compassion and forward-thinking than his father.  He too is a deviant, so maybe he understands.  David can read minds, and after what happens with Sophie, he shares with Rosalind and his other empath friends his perceptions on abominations and the true image.

I tried to explain that a person with a deviation -- a small deviation, at any rate -- wasn't the monstrosity we had been told. It did not really make any difference -- not to Sophie, at any rate. (Ch. 6)

As soon as David's secret is known, he will also be forced to flee.  His father does not care that David is his son.  In fact, it makes him more determined to see "justice" done and follow the law he so vigilantly enforces.

Another example of the horror of David’s father’s imposing religious doctrine is the baby.  David’s aunt Harriet brings a week old baby to the house, which does not have a certificate declaring it legal.  When David’s father asks about the certificate and finds out there isn’t one, his wife (whom David has already said is afraid of his father) asks to see the baby, while her sister protests that there is not much wrong with her.

'Nothing much!' snapped my mother. 'You have the effrontery to bring your monster into my house, and tell me it's nothing much!' (Ch. 7)

David’s father launches into a diatribe about why the baby is dangerous to their entire way of life, while poor Harriet, who has already lost other babies for apparently the same reason, cries and begs.  Joseph does not relent, telling her in “your arrogance you have set yourself against the law.”  He would turn in his own sister in law, and make her give up her baby.  David never finds out what is wrong with the baby, but his aunt kills herself.

These examples of religious zealotry and cruelty show that while the people are afraid, because of what happened to their ancestors, they have done away with compassion and common sense.  Instead, fear and fanaticism have taken root.  The fate of Sophie, David, and Harriet's baby are all examples.