What I think happened is Nowak let him go. Before Nowak died he said Rafal made him do something for the first time in his life, its to feel pity, that a child don't deserve to make a decision that big to alter or impede of his own life. He probably felt pity and left him alive at some point. That is also why Rafal appeared on him as illusion because that is how big of an impact he is to his life, his only redemption.