I don't mean to be insulting, but at this point I have to say that to me, that was a pretty weak argument in defense of violence in a film. Just because it takes place in a virtual world doesn't mean it wasn't real. Maybe it wasn't real in the literal sense, but it still happened. First of all, the effects are the same...everytime a person is hurt or killed in the Matrix, they die in the real world. As explained in the first movie, the Matrix is a projection of the mind, and the body can't exist without the mind. Everytime a person dies in the Matrix, the machines lose one more person to control. And besides, from the standpoint of it being a film, we as the audience SEE violence. It doesn't matter if it's something taking place in the mind or in a dream, the message is still being delivered through violence. It would be equally blasphemous to claim that Jesus fantasized about murdering hundreds of Romans even though he didn't. Secondly, just because the agents are evil towards humans doesn't make it right for Neo to destroy them...evil begets evil. Did Jesus go and slaughter the Roman emperor or his soldiers for their injustice against the Jews? No...that was part of Jesus' message as I understand it. Violence was not the answer.

As for religion being the scapegoat in war...it doesn't matter whether or not it was the explicit reason...to do something "in the name" of something is to make the claim that that something is the reason, whether it really is or not. "In the name of humanity, you must die." It doesn't matter if that person is really killing someone because humanity deemed it necessary, it's what he says. You can say you're killing someone in the name of the king, but that's not necessarily the real reason you're killing that person. So what I said is true, wars have been fought in the name of religion, even if the real reasons were political and economical. As for government killing its own citizens, that's the case in "The Matrix" as well...the machines govern the planet (or rule, whichever term you want to use, it's all the same these days) and they use and abuse their human citizens.

Again, I don't mean to be insulting, but I find your argument to be less than convincing.