Lethality!

How lethal to be can be a major decision for shadowrunning teams. On the one hand: dead men tell no tales. On the other hand: murder gets investigated!

Certainly the ideal shadowrun (for the runner) is to sneak in, accomplish the mission, and sneak out, with no evidence left behind (including astral signatures- use cleansing!), and no one seeing you.

Things rarely go that well.

If you're being recorded (video surveilance), watched (astral perception), or otherwise seen by things you can't take care of (or have reason to believe that you will), using non-lethal force is best. For one thing, it doesn't matter if the bad guys see you if you're already on camera, so why add (multiple) murder to your list of crimes? On the other hand, stun damage heals faster- so use discresion. Also, being the one guy on the team to use non-lethal is probably not going to make much a difference to a jury.

If you're sure no one else can see you, using lethal force becomes an issue of morality, but keep in mind that people will hunt down murderers. Extraterritoriality means that it's the company's "job" to look for you, and they may or may not want to "waste" resources tracking down a murderer. However, they could have agreements with local police (lone star) to find you, and the UCAS may be willing to "extradite" you to the company. After all, who wants a murderer living in their city?

Generally speaking, a single murder should increase the heat that you have to evade by 1 level, and multiple murders by 2 or more levels (or more if you blow up a building or something extreme). The GM decides what these "levels" mean, but it may be increased TNs to get away, or bonus dice on the part of law enforcment (or corporate security) to find you. This can be worse if you were photographed or otherwised winessed.

Keep in mind that dumping an identity is only really useful if the shadowrunning identity goes with it. (They can always try to set you up- see after the mission). Dumping a shadowrunner identity may lose you the benefits of your reputation, unless someone connects you to that identity.

Lethality may be less of an issue if no body is found. People you've tortured, kidnapped, etc may be able to provide information that only killing them can keep safe. That becomes a whole other issue.

Ultimately, lethality is up to you. Here are some alternatives to using lethal force:

Memory Wipe: Hooray for Mages! If they can't remember you, they haven't really seen you, though a good mage can beat this with mind reading.
Drugs: Some drugs cause memory loss, which can be the mundane's way of accomplishing memory wipe. Still suseptable to mind reading, and might not work as well.
Disguises: This can help avoid the issue of being identified- though using a shadowrunner network to locate you is not affected by this if you're reputation is increased by this mission.
Blackmail: Not always effective or available, but people are less likely to spill their guts about you if you are able to get revenge later- either by passing on secrets about them, or hurting their loved ones. This is the main reasons big companies don't get ratted out by each other. Ah, masquerade!
Stealth: (yeah, no kidding, right?) Of course, if you can knock them out before they see you, there's no reason to kill them.