Well done indeed my friend. However, in my opinion the first sentence of your post belies the entire scope and thrust of Halo from the viewpoint of Master Chief. Commander Sarah Palmer hasn't got a clue what's really going on and shouldn't have any command authority over Master Chief at all. (remember when cpt Del Rio tried to tell the chief what to do).
His orders (if any) would be from a much much higher source or, more likely considering the stories direction from his own volition and loyalty to Cortana, Earth, and Dr Halsey.