Social mechanism example : In Medieval Europe (and probably many other places and times) when a person commited a sufficiently heineous crime (or pattern of crime) and wasnt caught&punished , they were declared 'Outlaw' - someone who by their actions puts themselves outside of recognizing and following the common laws. A critical aspectg is that by putting yourself outside the law, you also negate your implied protection by the same (system of) law. An Outlaw could be killed by any man without penalty, and anyone who helped the outlaw was subject to severe penalties (thus depriving the 'outlaw' of the society the laws make possible). A decent repercussion/loose punishment , particularly in a world where organized lawmen were far between.
How do you implement a system like that in a game? A whole lot of behaviors supporting that system need to be created, quite general and versatile for all the things a player might do if allowed to largely 'do what they want'. Large parts of your simulated society would have to react 'appropriately'. You can abstract it some and subset it within the parts/aspects of society/ecosystem the game will simulate. We have a game industry universe where so much (still) has to be pre-canned/heavily choreographed, and the least little AI generality is touted as a major advance (ie- Half-life, a game generation ago) due to the combinatoric explosion of appropriate handling logic (to simulate 'morality' or social conventions) for any kind of game complexity (even trivial human simulation). Its no wonder the game industry is largely stuck and can give us few opportunities for real (cohesive) morality decisions in the games.
"Sorry you cant do that" for the least divergance will be with us for quite a while yet.
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?
Meanwhile 'safe' (not subject to morality based repercussions) filler is served up to keep the player busy.