John is freer than a World State citizen because he is capable of feeling a full range of emotions, including sadness. He doesn't just pop a pill the moment he starts feeling anxious. Because he is able to feel all his emotions deeply, he is free to intensely love the few individuals he feels close to, such as his mother, Linda, and to mourn for them when they die. He has also been exposed to literature and religion in a real way, reading Shakespeare and growing up in a religious tradition that is a hybrid of Christianity and Native culture. He has been allowed to feel pain and suffering and some of the magnificence of loving deeply. These are precisely the experiences that have been excised from the World State in favor of security, stability, social harmony, and a superficial happiness based on stunting and chaining the human spirit.
John, however, can be as much a victim of his own social conditioning as any member of the World State, especially in terms of sexual mores. He is as judgmental and unable to understand Lenina's free sexual giving as she is to understand why he would think she is a whore and a strumpet for sleeping with multiple men. He has rigid notions of fidelity and how dying should be handled. He is so unable to navigate the shock of his cultural encounter with the "brave new world" that he dies by suicide. Death is a form of freedom, arguably, but it is not the best for a young man with much to offer the world.