In The Chrysalids by John Wyndham, what decisions does David make, and how do they conflict with his moral values?

It is necessary to first establish what David's moral
values are so that his decisions can be seen to accord or to conflict with these values.
Also, as you'll see, there are two levels of a person's moral values. They are the
values a person is taught by family and/or  school and/or society [note: these may not
accord with each other!] and the values springing from one's own inner character.
Briefly, in David's case, he was taught by father, school, and society that rigid
conformity to strict and unyielding rules that punish "deviance," which is physical,
psychological, emotional, or intellectual departure from a sternly defined norm, is to
be brutally punished and eradicated--utterly destroyed. This is reinforced with slogans
like "The Devil is the Father of Deviation."

One decision
David makes that conflicts with the moral values he has been taught--his public
values--is to keep Sophie's secret about the deviance of her toes a secret--even at the
price of severe punishment. On the other hand, this decision accords with his private
values that only emerge and reveal themselves as he acts from inner impulses as events
come upon him. Therefore, while David's decision conflicts with his public values, it
accords with his private values, which are values he couldn't have known he had until
that event occurred. Another decision David makes that conflicts with the values he has
been taught is his decision to keep a secret with Uncle Axel about David's own secret
related to his cognitive powers. He simultaneously makes another decision that conflicts
with his public values and that is to keep the secret of his friends' similar cognitive
deviances.

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"Wouldn't it be more fun to do your chattering
with some of the other kids .... than just sitting and talking to
yourself?"
"But I was."
"Was what?" he asked,
puzzled.
"Talking to one of them," I told him.
...
"Who?"
"Rosalind," I told him. ...
"H'm -- I didn't
see her around," he
remarked.

Secrets are against
the moral values of the community since secrets may hide deviance and secrets about
deviance are paramountly against the moral values of the community since all deviance
must be destroyed. However, this is another instance when David's decision accords with
his emerging private moral values just as his decision to protect Sophie did. Two things
that clearly emerge from examining some of David's decisions and how they conflict with
his moral values. The first is David has two sets of moral values and they conflict
against each other. The second is that David follows his emerging private values at
great risk and personal hardship thus causing greater conflict with his taught moral
values.