Morality in video games

Most games that feature a morality mechanic either let you be Super Jesus from the planet Kantian or Caligula mac Nietzsche.
Usually represented by a sliding scale where being generally nice for a while can make up for burning down an orphanage.

Divine felines indeed.

But what would be a good way to represent a rational morality in video games?

What kind of choices could be put in such a game?
Do you have any ideas for a mechanic to replace the karma barometer?