system
Given the following post, respond as if you're commenting on Reddit:
human
In "The Matrix" did the protagonists kill programs or other people plugged in?

Especially in The Matrix 1. While we know that the crew of the Nebuchadnezzar (and the rest of the freedom fighters who can jack in) were at one point being battery farmed by the machines, what about the people they have to kill in The Matrix itself? Are they programs, like Agents? Or are they also people being farmed, potential Red Pills like Neo and Trinity? I don't believe this was ever explained.
gpt
Agents who take over the avatar of a blue pill do not die when they are sufficiently damaged, the blue pill might not be so lucky.  If you die in the Matrix, the body dies in real life.  

Some programs do not take over a blue pill avatar and simply have an avatar of their own, this is true in most cases of a program in the Matrix.  However, programs whose avatars are killed don't necessarily die permanently.  Remember, the Merovingian managed to delete the avatar of the Oracle and she managed to find a new one with which to manifest in the Matrix.