In The Matrix, it's clear that it's humans vs. machines. However, Morpheus and the others are constantly killing humans that are 'employed' by the agents. Sure they're fighting for their lives, but those people are clueless as to what's going on. So why, if the disconnected humans are trying to save the human race, would they have little to no issues with killing fellow humans? Wouldn't it make more sense to simply incapacitate possible future soldiers in the war instead of helping the machines by killing the humans?
The best explanation we have for the willingness of Zion operatives to kill humans plugged into the Matrix comes from Morpheus, during the Agent training program (emphasis mine):
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... [The Agent training program] is another training program designed to teach you one thing: if you are not one of us, you are one of them.
It is pretty clear that Morpheus considers blue pills to be their enemy and that the blue pills are, in a sense, actively fighting to protect the Matrix.
The idea to incapacitate blue pills doesn't seem like it would work. Agents are free to possess any blue pill because they are hard wired to the system, and it doesn't matter what state the blue pill is in.
A case where a Zion operative might have had the ability to incapacitate a blue pill (rather than kill him) occurs in the Animatrix episode A Detective Story. In it, Trinity is meeting with a detective when an Agent starts to take over his body. Since it takes several seconds for the Agent to fully possess him, Trinity may have had time to knock him out. Evidently she did not think this would make any difference because she shot him instead. This stops the Agent from possessing the detective's body and allows Trinity time to escape, but probably resulted in the detective's death shortly after.