You are right, you have to take exercising a day at a time and you have to listen to your body. As long as you are doing something (in the form of exercise) every day, that will help you more than you realize.
With reference to diet and Lupus, there are some who believe that an improper diet can exacerbate Lupus. Then, as you've discovered, there are some who don't think that there is a connection between the two. You have to learn YOUR BODY and what helps you and what hinders you. If certain foods seem to worsen your symptoms, eliminate those foods. It's just that plain and simple, regardless of what your doctor may think. If it affects your body, it affects your body weather he believes it or not!
Now, he may be right in thinking that diet does not cause Lupus. However, as I mentioned before, some foods can make symptoms worse in some patients. The goal of treatment in Lupus is to lessen and/or eliminate symptoms. You must do what is right for you, so if adding holistic modalities to your treatment regimen helps, then continue to do so.
Peace and Blessings
Look For The Good and Praise It!