I initially posted this under Dark Avatar, but I figured this would beneift the original as well.
I was thinking that somehow your civilization's morale should be more dependent on many more factors.
For example, suppose you have been allies with another civ for a majority of the game and you then decide to back stab them for a military victory. There should be a morale penalty for this. Something like this today would take your citizens back wondering why their country's buddies are now their enemies.
This could also work for ethical alignments and the such. If you have constantly been choosing the Evil option on the random events, there should be a morale penalty if you decide to buy your way into being "Good." If a civilization is used to being evil, they would have an awfully hard time suddenly changing to live good lifestyles meaning they would not be please with their government for the change.
There could be many more instance if morale was decided to be used this way. I'm only trying to brainstorm right now, so everyone else's opinions are certainly welcomed.