I just discovered this great website. I actually loved the idea of Zakos even before I knew the name "Zako" existed. I'm more into Zakos in anime and live action and less from games.
I have a bit of a different view on the Zakos' background. I like the concept of them not necessary being evil. Instead, I like the idea of them being average young women who took the opportunity for a decent paying job where they got to wear cool/sexy uniforms and where they really didn't expect trouble because they didn't realize they worked for an evil organization.
They have families and boyfriends. In fact, I like the concept of their lives outside their job making them sloppy and subject to being taken out. Perhaps the girl is busy with a cell phone call with the boyfriend so she doesn't realize she is being snuck up on. Or she falls victim to the hero's pretending to flirt with her.
They are your cute girl next door types. They are not particularly skilled or bright so they are easily taken out and rarely put up any kind of fight.
Given that they are basically not evil, I like the concept of them being just knocked out. I don't mind them being roughed up a bit but not killed.
As some others have stated I like it where we see them laying there while the action goes on around them and nobody seems too concerned about them. However, I do occasionally like someone coming along and checking the girl's pulse to confirm she is just knocked out.
I also like the idea of them being dragged off to be hidden, searched and sometimes having their uniform stolen so the heroes can sneak in.