Stonewall was shot in the arm by his own troops while inspecting the battlefield after the battle. Ridiculous accident....
They could never have won the war completely on the battlefield and I think Lee knew this. His hope was to wage an aggressive war against the Union troops in the East and drive as far Northward as possible. If he could have destroyed that army then the picture would have changed drastically.
The greater issue of the Southern Cause was a loser from the start. The 'way of life' was doomed in the long term, as all backward, static social and economic systems are.