Well this seems to be because it comes down to politics and a very unintelligent group of people in the masses. Sometimes doing a "bad" thing is actually the right, or "good" desician, something that MOST stories do not touch upon.
To put it into perspective, mass murdering people (especially civilians) is considered to be "wrong" because it leaves a lot of people dead. However in many cases it's really the only way to change things, and you can see the problem with being too quick to preserve human life when it simply amounts to a cycle of endless enimity with far more deaths over a long period of time when peace (and less deaths and hardship) could be achieved by simply killing a whole lot of people at one time.
It comes down to the mentality between "police actions" (which we currently call wars) and actual wars which were fought from the beginning to permanantly resolve problems.
Heinlan touches on subjects like this, assasination, and other things in his writings.
Or to put it into perspective of my ethics classes many years ago "It's easy to argue against morality by the numbers, as long as the numbers are small enough". It's easy to hate on the man in charge for doing bad things to a lot of people (especially when your one of them), but oddly it doesn't mean that if you were in his seat, with his perspective, that
you wouldn't wind up doing the exact same things due to a big picture most people either do not see, or intentionally do not want to see.
The closest video games TYPICALLY get to situations like this is like in inFamous where you have to choose between saving your girlfriend, or multiple doctors. We know what desician the game decides is "good" but on many levels I tend to disagree.
It also comes down to politics. A couple of times when I was listening to Henry Bendix "getting his evil on" in "The Authority" I was kind of like "well he IS right you know".
At any rate, a lot of it comes down to politics and social philsophy as well. Any discussion about good and evil, or right and wrong tends to develop on so many levels that your never going to get everyone to agree on anything.
That is also one of the major reasons why in many cases that guy who is the "evil Overlord" (ie the buck stops with him) it can be hard to judge, because he's going to do something, and chances are if it got that far to begin with, it's not a black and white problem.