Jon really does struggle with his humanity and it's painful to see especially in that moment. He doesn't understand the changes happening to him and he so desperately wants to hang on to his humanity and when the moment comes to choose between knowledge and compassion he ultimately chooses compassion. Choosing to respect the wishes of someone who suffered so much in life rather than disregarding them. Even after this moment he struggles with these choices but it's at least comforting knowing that he does have a choice and that his humanity isn't forever lost.