Don't get me wrong, making a game where even morality is dynamic would be neat. To me, it would be awesome if Fascism wasn't hardwired with forced relocation -- who says it has to be? To me, it would be awesome if Democracy wasn't hardwired with war weariness -- who says it has to be? To me, it would be awesome if you could span the entire game without discovering ecology, or a united nations, or democracy, or even monotheism.
But let's work with what we have. It's fun to talk about Civ 5 or 6 or 7, but looking at Civ 4, I tend to focus more on what we can do in the short term, with the long term there more just to inspire vision.
If you did hardwire some moral progress, you could actually make new game conditions and goals to work through.
There are several "inevitabilities" that we can "count on".
Globalization -- a sense of a global community that scrutenizes one another.
Expanding Religious Thought -- more people who see all religions as leading to the same place, instead of something that divides people.
Modern Global Warfare -- the after effects of war become more widespread and brutal.
Mass Media -- in the age of information, people can get a sense of the realities of war and the world.
It's then no doubt that you can have mass amounts of peace-loving people against at least SOME war, and who see the aversion of genocide as a good thing. (That is, of course, if they NOTICE the genocide.) For many people in many nations, they become very upset when their governments refuse to do something about mass amounts of death. Governments thus make it a goal to encourage peace and human rights around the world.
The key word is goal: governments make it a goal to "do the right thing".
Now this doesn't have to totally ruin the game for everybody. I'm not talking about branding any nation who goes on world conquest evil. Nor am I talking about those who ignore genocide as getting bright flashing warning messages from their AI-programmed conscience. All I'm saying is that by the modern age, doesn't it make sense that averting genocide makes you considered a hero? To lay it out simply, one thing that makes the modern age so interesting is that people ARE trying to do "good things".
In Civ, there's no encouragement to do so, because war is always seen as amoral and selfish. And in making a game amoral, it actually indirectly makes the game anti-historical. You couldn't explain the past 50 years of history if you didn't believe in the most simple of rights and wrongs.