Ever since I could read, I was always like your son. I am very intelligent, but my emotional state and physical age, as your doctor said, is far behind my intellectual capacity. For example, when I was in first grade, a tornado watch was in my area, and I just freaked out at what I saw on the screen. All of the sudden, I was yelling, "WE'RE GOING TO DIE!" repeatedly, and my mother eventually got frustrated with me. At that same year, I also "discovered" medical textbooks, and when I read them, I got a fear of tetanus, whooping cough, diptheria, rubella, strokes, and comas.
Your son could benifit from cognitive therapy. If your son is used to the statistics of a tornado appearing in his state, he'd be gradually habituated out of the fear. Plus, cognitive-behavioral therapy doesn't dissipate your child's natural personality with medication or other treatments like that! It just makes the fears naturally go away. It worked for one of my fears, and if your child is tired of being scared, it would work out.