when humans are killed while jacked into the Matrix........their bodies to still exist in the Matrix. Watch the first movie when Apoc and Switch are unplugged/killed........their bodies collapse on the floor and stay there. Their bodies are still in the matrix.
Neo is different.......he is not just human. He is part machine......he has the code of the anomolous program inside of him......and like I said, what happens in the Matrix when a program is killed? It returns to the source.