It seems that there is no question that David pays a price for choosing to live as he does.
In John Wyndham's The Chrysalids, the young David at the beginning of the novel is unsure as to what is going on around him, how the world can be so upset about things like "extra toes," and why he must keep his knowledge and his abilities to himself. There is a certain irony in this as his father is a leader of the movement to exterminate all "mutants." Though surrounded by it all his young life, as is typical of human nature, it is sometimes impossible to fully appreciate something one sees and hears every day until it affects us directly.
David's first exposure is to the secret he learns and must keep regarding Sophie's extra toes:
"It's very, very important," [Mrs. Wender] insisted. "How can I explain to you?...If anyone were to find out they'd—they'd be terribly unkind to her."
David promises and keeps the secret. However, when Allen discovers the secret seeing the extra imprint of Sophie's wet toe on the rock at the water's edge, David learns he must take a stand, though he is still rather young. He fights Allen (though he loses badly) simply to buy Sophie more time to evade capture. David then warns the family that they have been discovered, and—at their request—takes his time getting home in order to buy them more time to escape.
Taking these actions makes David feel alienated from his family and society, for he has turned his back on what they believe to save a friend. (And he hears about it when he gets home.)
David is further alienated when his uncle realizes that David is telepathic. Knowing his nephew's danger, Uncle Axel protects David (and Rosalind, who David communicates with using his mind) by warning the boy of the dangers of being found out:
I want you to keep it a secret. I want you to promise that you will never, never, tell anyone else what you have just told me—never. It's very important: later on you'll understand better how important it is. You mustn't do anything that would even let anyone guess about it. Will you promise me that?
When the word gets out that David and his friends are telepathic, and that his sister Petra is especially "gifted," David must sacrifice the comforts of home (though not any sense of love from his family, even his mother—they show little concern for him) to escape punishment and death. So he travels with Petra and others to find a place where they will be safe. The journey is not without dangers; besides pursuit by the members of Waknuk (David's town and home), the people of the Fringes—outcasts like David and his group—are also an enormous threat—they have become violent and predatory even with other outcasts such as David and his companions.
David does pay a cost for choosing to be different and protect others, but they are all saved (except for Michael who stays behind to return to save Rachel) by people on a flying ship from Sealand (New Zealand)—the place of David's dreams when he was young. He no longer must keep secrets and live in fear. Being different is nothing to fear, but something to be celebrated. In the end, the sacrifices David has made are rewarded, especially in trying to keep those he cares about alive and safe, making every risk he took worthwhile. It's the kind of person David is, and his choices reflect the kind of character he has.