That's funny, I've recently started taking note, for some reason, of the amount of people you actually kill in video games. With the Shinra army being a good example. Pretty much everyone here is right.
Chances are they didn't kill every last opponent in their way, they probably just incapacitated several, and not necessarily on purpose. For example, when they were raiding the Junon reactor, they were moving fast. In all likelihood they're running by, some troops raise a gun at them. Barret fires a few rounds or Cloud slashes, the guy falls out of the way and they keep moving. The man could very well have taken a round to the shoulder or a slash to the arm that simply knocked him over.
Obviously, they also face real opponents that stand their ground would have been cut down, or Vincents bullets and Cid's spear simply hit home and killed someone.
It's why I think, were they to make another RPG-style game following DC, it would be interesting to see how the world regards them. We know they're regarded as the Heroes of the Jenova War, but apart from the rich folk that lived on the plate and lost their easy electricity, I would imagine there are many many families of Shinra troops that AVALANCHE killed and might even hate them.
I always spared the guys on the sub, they were your friends from the Junon parade! I wasn't gonna kill'em.