Think about this. What if switch, Apoc and the others are not dead.
Now we know that there is a hierarchy in the Matrix.
Now ask yourself this, are the humans in the Matrix really human? Or are they lower level Programs?
In the real world the hierarchy would be.
As burlyman has stated that the Humans need hardlines to get in and out of the Matrix. The lines are used to separate the body from the mind.
While they are separated the Human mind becomes a digital repersentation of the physical self.
That digital representaion is PROGRAM. It may be a low lever one, but a program none the less.
Now Morpheus told Neo that the body can't live with out the mind. Was that the truth?
The better question would be can the mind live without the body?
True self-knowlege is the key.
A good example of this would be Agent Smith/Bane.
Agent smith was a program that had full knowlege of self. He didn't need a body inorder to survive, but he needed a body to crossover into the real world.
So as we all know Smith used the hardlines inorder to pour his digital image into a physical body.
Now that Smith is in the real world he is subject to our weaknesses. If his body is killed he will die because his digital self has nowhere to go, unless he reloaded himself back into the Matrix before his last breath.
Remember he has self knowlege, so he would live on (in the Matrix) with out Bane's body.
The samething would also apply to Neo.
At the end of Reloaded Neo noticed something different. He knew he was still connected to the Matrix.
In M3 we find out that Neo is still connected to the Matrix because his life signs still show him to be jacked in, even though he was still in the real world.
Before Neo passed out at the end of Reloaded He knew he was still jacked in.
True self-knowlege is the difference.
I guess that's why on the ship Trinity's light is Blue while Neo's is red?
Anyway getting back on point.
If Switch, Apoc and the others had true self-knowlege they may not have died when they were unplugged.
The Orcale stated that when programs are done their jobs they are to be deleted. Now keeping this in mind. The body can't live without the mind, but the mind can live without the body. The digital representaions of Switch and Apoc were deleted, because their digital images were in a way a lower level programs. Had they known, they could have resisted they might have lived. Who knows they might be saved on a huge digital database somewhere in the martix (That was speculation... Well all of it is Speculation
Remember what Neo said at the end of M1.
They all can't be the One so IMO self-knowlege is the key to this puzzle.
Even the main Cast is still oblivious to the truth. Neo will learn the full truth. Even now his knowlege of self has surpassed even Trinity or Morpheus's Self-knowlege.
Neo will teach the world the truth through his last actions.
Who knows he may disperse his code through out the whole of the Matrix. In essence making everyone the one. They would have his knowlege and abilities.
Its not impossible because everyone who is still jacked in, is stll a program as stated before. So speading his code is not so far feched.