Agent 47 is a man with superior skills after a life of nothing but guidance. His entire life with one purpose, a questionable purpose. So much so that his final mission is to put an eternal end to the program that created him, including eliminating its creator and his daughter.
However, something changes when the two are united. Instead of killing her, he takes her under his wing by protecting and teaching her. The humanity we are believed not to exist in him makes a full broadcast.
It begs the question. Can a man truly be stripped of his conscience and ability to make choices? Our ability to make choices is what makes us human. Free will is a gift from God. This allows us to think for ourselves. Make our own conclusions. Answer to our own conscience. Live our own lives.
Without it, we may as well be God's little puppets. We are not puppets. Not to any person. Not to any organization. Certainly not to God. Agent 47 is a story about two people who discover their free will and take control of their own lives.
Just like Agent 47, we are called to evaluate our lives, repent, and make changes. Agent 47 makes a choice to cherish Katia's life instead of ending it. Though he disobeyed his orders and lost his job, he is granted a partner and the chance at a real life. That is something on which you cannot place a price tag.
Sources: Fox Movies, IMDB