You bring up some excellent points. First of all, I agree forcing your mind into thinking positively will not really accomplish much. There is a difference between thinking positively and living with a joyful and loving attitude. We need to change the very way that we are and the way that we perceive life.
I also agree with your point that most disease comes not only from our everyday thoughts and stresses, but also from unconscious (or subconscious) repressed and traumatic memories and emotions. If a disease is caused by something in the subconscious it must be accessed and brought into our conscious thoughts so that it may be dealt with. This is the idea behind psychotherapy, hypnosis, and other methods of accessing the subconscious mind. These repressed thoughts and emotions may also be accessed through meditation.
The idea is not to deny reality, the idea is to change your reality.