As you might have noticed, I can be a bit opinionated and one of the things that drives me nuts in Shadowrun are players that think killing NPCs is the only way to handle them.
As a full disclosure thing, I have played a very pink mohawk character that did kill a lot of people. However, the situations were either in the Barrens, on a wetwork job, or when hopped up on kamikaze.
The typical Shadowrunner is supposed to be a specter, a crew of high tech criminals that can do jobs that the average Joe off the street wouldn't have the skills, know-how or resources to pull off. These are the type that could steal Canada's Global Strategic Maple Syrup Reserve and escape clean.
Well, almost. As I have said in the past things never go as planned and typically one of those nevers happens to be running into a guard. OK this is no big deal, the typical corporate security's job is not there to kill a runner, or even to stop them. Their job is to _delay_ the runner until the HTR boys can get there and handle business. They know they're not as well trained, or well armed as the runners they come across. So they try to slow them down and keep themselves alive.
So there you are, four badass runners facing off against Officer Doughnut. There's several was to deal with him, but before you can even twitch the Street Sam cleaves him in half with a battle axe.
This is where things go south quick. A corporation will sort of gloss over you knocking out Officer Doughnut. Sure, he might get a demotion and there will be a disciplinary hearing against the whole security department for that facility. However, that is just business as usual for a Mega. After all, if you did a good job hitting them this week they might be hiring you next month to hit one of their rivals. No harm, no foul. Sure they're going to make an effort to get their Whutzit back, but to them the runners are just tools not the hand that deploys them.
No, when you kill Officer Doughnut now the corp has several problems. They have to pay death benefits to Officer Doughnut's wife, grief counseling for his kids, training his replacement not to mention the internal PR issues they have to face. After all, if your company's security can't keep itself safe, who will keep the rank and file safe? Think of the kids!
At this point what went from a typical price of doing business in the 6th world to a "this is costing us real money" situation. As we all know, there's not many things a corp really hates than for its profit margins to be messed with.
So now the corp starts hitting back, they need to make an example of the team that bloodied their noses. They need to regain that internal confidence that makes their employees happy little wageslaves. So Mr. Johnson visits an illegal arms dealer to find out who's moved some of their stuff recently. Maybe they talk to the Fixer who hired you (what's that loyalty rating again?). If they find you and your crew, it won't be Officer Bagel that comes looking for you. It'll be the black ops division of the company, or their HtR crew depending on how public a message they want to make.
So really when you're facing down Officer Doughnut, unless the job CALLS for killing everyone (and pays a hell of a lot) tase him, stick-n-shock him, hit him with Narcoject or just have the troll bonk him over the head. Because killing him is going to cause you more trouble than a Doughnut is worth.