Well, this is Shadowrun, so bad things will happen to the runners sooner or later. Sooner more often than later, usually. So while they are fine with robberies and runs and even wetwork, it gets to a point where, if the crime is severe enough, (I.E. Women and children, or large quantities of civilians), the runners start to feel they deserve the retaliation that comes their way.
(Which they do in fact deserve. . .) but it usually results in fatalistic actions in a form of passive suicide for the character. Since the players are enjoying their characters, most will avoid these situations in an effort to keep the characters alive and in (realitive) good social standing. "Sure, I've killed folks, but I'm nowhere near as a bad as Nasty John Doe over there, go prosecute him."
That kind of mentality. Thing is mercenaries have a code too. But their code is professionalism. Do the job, no mistakes, and no complaints. Without a worthy rep, they get no work. It's just a different code from the standard sammie, or street avenger/vigilante.