I'm not sure it makes you atheist or hypocritical, I think it means you are confused and unfocused about what you believe. Any sane person would question a command from God to kill, but not many have stopped to think about what this means. It means you feel that you may know better than God. It means you are not convinced of his glory. It means you do not take to heart most of what the bible says (which we already knew). It means, above all, that you trust in yourself. Perhaps the God standing behind you and guiding your intuition is actually you. Perhaps it is your mind, your being, which is worthy of worship and glory. That might explain why, when you try to apply your idea of God to a practical world, you run into problems such as this. The feeling you have of God is real, but the image you have is simply a distorted and unrecognized reflection of yourself.