I think the key here is what type of game are you playing. What I am seeing from a lot of people, they are playing the game where runners are criminals, generally socipathic killer types with little remorse or regret. They are the people you call when you need dirty deeds done, and they won't lose much sleep when the time comes.
These are the same games where you have anarchistic type gangs setting up shop throughot the city, and the cops only care if it is someone under their jurisdiction. "Oh, there's a crime happening at that address? Wait, that's Ares territory, they'll handle it, but we'll place a unit in the area to keep them from doing the same to our clients." These are likely the same cops who'll take a bribe to look the other way. "No sir, I didn't /see/ anything illegal going on."
You kill someone, you leave them unconcious or you sneak past them, either way the corps are still going to come after you in some way, shape or form in a world like that most likely. Because you cost them, and if you cost them enough, they'll want you to make your money back. And besides, let's just think about what these corps have: Magic, cameras, security guards, drones, DNA, fingerprints. Heck, what's to stop a corp from putting out a few feelers and saying "Yeah, we're looking for some skilled people to go after some targets, sort of like the guys who did that Mitsu job a month back." Wouldn't be surprised if your fixer phones you and says, "Hey, got a job you guys might be good for", since the fixer sees it as an easy payday for them.
Now, not everyone plays in that same world. Some people play a world more like Robocop, where the cops actually care and will provide support. There was even a scene in Robocop 3 where the cops took off their badges, tossed them on the ground (all the while the OCP rep was going on about how they're putting their pension in jeopardy), and saying that kicking people out of their homes ain't work for cops. "Think about your family," says the rep. "I am," replies the sargent, "I'm thinking I have to go home and face them."
It is possible for runners to be criminals and still be the "good guys".
Amanda Hades is a web-based series about a decker, a face and a techie who are out to spread the 'truth' about the atrocities done. Sneakers, sure it was back in the 1980's, but it was a well-planned and high-performing shadowrun team who broke into people's places so other people couldn't break into their places. Boondock Saints is another group of runners who were doing 'good things', Hardwired is a recent movie about a shadowrunning team doing good. Push could be considered that way. Kung Fu: The Legend Continues is an example of how you can be a shadowrunner and not go directly on shadowruns. Kwai Chang Caine was a kung fu master, his son Peter, a cop. The two of them would go around and solve crimes, help people in need, take down the bad guys, etc. (It may be more work for a GM to craft a storyline this way as opposed to the 'corporate dungeoncrawl of the week' type shadowruns)
The body count doesn't make a team good or bad, but leaving people unconcious or sneaking past them is so much better for that rep. And good or bad is all an idea of perception, the corp views your actions as bad, but the people you're doing it for view your actions as good. The normal civilians would look at amanda Hades news hacks (much like Dark Angel's 'Eyes Only') likely as a hero, a champion of the masses giving them the real story (the ones who saw past the corporate bull coverstories, anyway). The people who Caine helped would be quite grateful, but the people who lost money and the like would be pissed.
You can also create runners who do the whole Robin Hood thing, but that's up to the GM as much as the players. I've had players that wanted to do that, set up a small community where people were welcome so long as they didn't cause trouble, and they would do runs for water, food, fuel, spare parts, clothing, etc.