What does the prison chaplain warn Alex about? Why does he disagree with the treatment?

The prison chaplain warns Alex to be clear in his mind about what he is about to undergo. He states that Alex will be made into a good person, but says that he personally disagrees with this type of treatment. In the Chaplain's opinion, a man who has the freedom to choose to be evil may in fact be better than a man who has good forced upon him.