How much do you think the death of Stonewall Jackson affected the outcome of the war? From what I remember, it definitely was one of the things that turned the war in favor of the North. Stonewall was a brilliant strategist and a hero to his men. His accidental death by friendly fire had to have affected the soldiers under him, as well as the Confederate leadership.
I think Jackson brought a sense of discipline to his army that was slightly anathema to the rest of the Southern armies so whilst everyone else made their names as cavalry men he seemed to understand artillery plus infantry better than anyone. It may also have helped that he had to face McClellan, an opponent that Jackjosn could only have dreamed of.