Arguably, the theme of friendship is the most important one in chapters 15 to 17 of The Chrysalids. The reconciliation of Sophie and David after all these years illustrates the unbreakable bonds of friendship even in the midst of extreme adversity.
By rights, Sophie and David should never have been friends; Sophie is a member of a despised minority, whereas David's father is one of the spiritual leaders of a society in which people like Sophie are routinely exterminated or exiled for their physical deformities. That they remain good friends, despite everything, is a testimony to the strength of their bond.
True friendship involves sacrifice, and Sophie risks her life to save David from the evil clutches of his uncle Gordon, the "spider-man." To some extent, the tables have been turned in the Fringes; now it's David who's the outsider, not Sophie; but Sophie has not become embittered by her experiences in Waknuk. Instead, she's developed a considerable degree of empathy. David is not the Other; he is a dear friend, someone she will do anything to protect.