What truth(s), or moral(s), can be gathered from having read The Chrysalids?

As a science teacher, one important truth that I believe The Chrysalids points out to its readers is the importance of genetic variation. Waknuk society is terrified of genetic change. People have simple sayings and reminders hanging up in their homes to remind them to be on the lookout for any genetic deviation from the norm, such as:

THE DEVIL IS THE FATHER OF DEVIATION

At the end of the story, the Sealand woman explains to David why Waknuk thinking is completely flawed.  

“The essential quality of living is change; change is evolution; and we are part of it.” 

I couldn't agree more. The advantage to a sexually reproducing species is that genetic variation is going to happen. Half a genetic code from each donor will help to create new code. Add to that things like independent assortment and crossing over, and the possibilities for new genetic code are nearly endless. The Sealand woman is emphasizing to David that change is good because it allows a better chance at living. She's totally correct, and her statement is the basis of Darwin's "survival of the fittest" concept.

Another truth that I think The Chrysalids accurately portrays is that people can be incredibly cruel toward and intolerant of anything that is different.

“I’m not sure that I know why," I told her. "But they are. It’s a feel-thing not a think-thing. And the more stupid they are, the more like everyone else they think everyone ought to be. And once they get afraid they become cruel and want to hurt people who are different—” 

The fear of people who represent difference leads to cruelty toward those people. It's the basis for racism and sexism. In David's case, it might be called something like "genoism." The Waknuks are fearful of deviant genetic coding. That's just ridiculous, but it is a common motif in a lot of modern stories. Take the X-Men universe, for example: The mutants are feared because they have an extra set of chromosomes. The movie GATTACA is based entirely on a society that discriminates against certain genetic types. The Chrysalids is another example of how people frequently mistreat others just because they are different.