I saw "Food Matter" and thought I'd jump in here! First, let me say that I enjoyed the documentary and frequently look at their material.
My thought is that I think when the speakers are talking about how we are destroying our food by cooking it, I think (my take/impression only)they are talking about how we cook our food currently...over cooked. For most people, when they cook vegetables, they cook them until they are soft and mushy. Cooking vegetables like that does destroy the nutritional content of the food. Lightly steaming vegetables is a great way to keep the nutritional content and help the food become easier to digest. I for one, cannot eat a large amount of raw broccoli because it causes stomach distress in a severe form but if I lightly steam it, I could eat a pound with no problem!
The Food Matters website also has recipes that call for cooking vegetables. If you look at their 3-day detox, they have a vegetable soup recipe that is cooked. Many raw advocates do lightly cook their vegetables and even fruits.
Hope my 2 cents helps a little!