Great point. I always thought they were kind of tapping into the "it's all just a video game" kind of vibe, but you are so right because even in the matrix universe this is just an abstraction because if you die in the matrix you die IRL. 

There is definitely also a hot war kind of mentality as well and as you point out, everyone who is still plugged in is essentially an agent. They also only kill indiscriminately when there is a greater threat of agents.  

I think as I've gotten older and also as I've gotten closer to God, I now find myself questioning the morality of any war movie including WWII movies like saving private Ryan, which also came out in a similar time period. But that was not my mental frame at the time.