system
Given the following post, respond as if you're commenting on Reddit:
human
[The Matrix] Aren't Neo and Trinity killing innocent people?

I watched *The Matrix* years ago and started to watch it with my son the other night. I was in and out and didn't see the whole thing so I don't know if there's an explanation and I missed it, but when Neo and Trinity storm the building to rescue Morpheus, they kill a whole bunch of ordinary security guards, then SWAT personnel. Aren't those regular people in their little battery cocoons thinking they're security guards and policemen? The agents are AI, I understand that, but aren't the non-agents regular people? When they get shot and thrown off buildings, they think they're dead, don't their actual bodies then die in real life?

In that same regard, the homeless man in the train station is "possessed" by Agent Smith, then presumably killed by the train. Smith walks out of the inside of the train, having jumped to another body. Since the homeless man believes he was killed in the matrix, isn't his body now dead in real life?
gpt
Everyone answered your question, but here is a quote from Morpheus which addresses the issue as well:

“The Matrix is a system, Neo. That system is our enemy. But when you're inside, you look around, what do you see? Businessmen, teachers, lawyers, carpenters. The very minds of the people we are trying to save. But until we do, these people are still a part of that system and that makes them our enemy. You have to understand, most of these people are not ready to be unplugged. And many of them are so inured, so hopelessly dependent on the system, that they will fight to protect it.”