I completely agree with this. In addition I'll say that if you put your players in situations where they are forced to make touch decisions that show the moral character of the environment they are in, you'll likely get a better response than if you just try to force it on them.
Exactly. Shadowrun -- like almost every other game system* -- rewards doing good things and making hard decisions in favor
of the good.** Don't put them into situations where they have to choose the bad; make the 'bad' to be a more merciful and good (if more
personally damning) choice than the 'good' one. Kill one captive so that he won't kill one more, or many other people. Do the job, wiping out the scientist's memory, because that was the deal and if you don't then you are breaking your word.
And if they choose 'merciful over honorable', as in the second example, punish them for it. Bump up their notoriety as Johnson spreads the word. Have their contacts start making jabs at them about 'so when are you gonna screw
me over, huh?' Introduce them to the fact that 'professional' does not mean 'pacifist' -- it means you do what you say.
* --
Please don't start listing the ones that aren't.
** -- This is in part because of how people have to deal with real life, where there are few clear-cut (or even muddled but discoverable) good/bad decisions. In essence, we want to be good people, and be directly rewarded for it, which is the part we usually miss out on IRL.