Sophie means that anyone who is different is going to be hurt, because society ostracizes them. They will never completely fit in, and they will always be afraid.
When David and Rosalind escape to the Fringes and David is reunited with Sophie, they have a conversation about deviation.
'It's difficult to explain. But it isn't all wonderful. It can hurt a lot sometimes.' (ch 15)
Sophie tells David that anyone who is a deviant hurts. She probably prefers his deviation to hers because no one can see it, as opposed to Sophie’s extra toe that anyone can see.
This is another example of how unchanging the society is. Sophie and her family had to flee, and the situation for her seem dire. She lives a harsh and difficult life. It’s hard to say that the new society is more cruel than the one they left, but she definitely does not fare well as a breeder.