I understand the over thinking things because I have done that myself, but I have realized that over thinking is a bad thing to do. Well, at least when I do it I imagine things that obviously are not true cause you do not know what someone else is thinking. In your post you remarked several times that you were going to leave your friend alone, but it never seemed like you did.
He told you that talking to him when he felt like that did not help but you did not like that answer. If that is What He Said then maybe you should listen rather then pushing it! I would not take your name off his friends list or any thing like that. Just let it go, if he wants to be your friend and you are still interested you can decide then. Just let him be!!!