In The Chrysalids, can I say that the end justifies the means?
This is a fascinating question to consider when discussing this novel. Of course, the big question that is not made clear in your question is, "For whom?" In this dystopian novel we are presented with a number of different groups of people, each with their own interests and motives. Quite clearly, for the Waknukians, the end of achieving genetic purity does not justify their means of torturing and forcibly sterilising any deviants. Real ethical dilemmas are raised too by the people of the Fringes, who invade the territory of the Waknukians and kill. They need to do so to gain food and crops, but is it justified? It is hard to answer affirmatively.
Then, we have the group of telepaths, who are forced to run away and kill to escape. Arguably, you could say that the end does justify the means for this group, as the Waknukians have already shown themselves to be absolutely unsympathetic towards any deviants, as their torture of Katherine and Sally illustrates. Sparing Petra that fate would point towards murder as a way of escaping. Lastly, and perhaps most interestingly, we have the Sea Landers, who kill all the inhabitants of the Fringes and the Waknukians who are attacking them indiscriminately because they are an anachronism of humanity and will perish eventually anyway. They justify this "means" through the saving and gaining of Petra, and yet to the discerning reader, the motives of this group should ring alarm bells, as they seem to demonstrate the same kind of prejudice and violence towards the Waknukians as the Waknukians do towards deviants.
Thus your question depends greatly on which group you are talking about and your own moral assessment of their motives and actions.