One of the most important quotes in this book comes from the writings of F. Alexander, which Alex reads before he beats up the writer and then rapes his wife. F. Alexander has very strong notions regarding society and what should and shouldn't be done by society in the name of trying to create peace:
The attempt to impose upon man, a creature of growth and capable of sweetness, to ooze juicily at the last round the bearded lips of God, to attempt to impose, I say, laws and conditions appropriate to a mechanical creation, against this I raise my sword-pen.
F. Alexander therefore criticises the way in which his society is trying to limit the freedom of individuals, even bad individuals, through the use of technology. Alex initially ignores this passage but he later returns to think about it when his own free will is something that is stripped from him by the state.
This quote, and how it relates to the novel, makes it clear that this is a story that is essentially about the importance of free will. For us to be human, Burgess seems to argue, we need to have free will. For us to have free will, it therefore follows that we have to acknowledge that some people may choose evil rather than embrace good. Alex is of course a classic example of this. Trying to take away somebody's free will, which is what happens to Alex, makes him less of a human.