Of course the OP was asking about games having 'compatible' morality and the effects of not being compatible , but do we yet even have the ability to handle anything more than a prefabricated (staged) 'act' (the player is allowed to do) and a corresponding completely choreographed response/reaction?
Yes, but only if we are willing to peek behind the curtain, and analyze what makes morals moral. If "Morals" only refer to remembered morals, as socially agreed upon in the real world, then only those pre-set morals that have already been identified and classified as morals are allowed to be in the set of all morals. So there can be no further development or engineering.
What are the component pieces that make up morals? Why is one action "moral" and another action "immoral"? In our culture, murder and racism is considered immoral. But in video games, murder and racism are normal behaviors of a player.
Age of Conan implemented an "outlaw" status; if the player committed game-defined crimes, their access to NPC vendors changed, city guards would attack them on site, and other PvP players were awarded prizes for slaying them. The PvP players who performed those game-defined crimes screamed bloody murder on the forums, saying they didn't want to be penalized for playing the game their way. The outlaw status then went through a few patch changes and modifications.
Space Rangers 2 also has an outlaw status of a sort, in that the player may choose the life of a pirate wherein they rob and pillage civilian space ships. But the consequences are light, with police not particularly threatening, and the ability to buy off most politicians quickly and easily, and benefits of access to pirate bases.