Right now a civilization morals are pretty much set in stone from the moment they exist and hate crimes are non-existent, so I suggest a way to add those things to the game.
Basically it would work with historical events, if a blonde dwarf became a bandit and slaughtered a village or a great hero/king had a grudge against a homosexual courtesan the civilization could start to "dislike" those traits, with could lead to the affected dwarves having less friends and therefore a higher chance of becoming criminals, with would lead to more hate points to that trait, etc. Finally we have a civilization that hates a certain attribute, even if the original reason has been forgotten. This could also include things like being tall, cowardice, having a different colour of skin, being a sadist, liking nature...
These attributes can only be hated if they are the minority of the population, the point is that they are trying to blame the problem on a unusual trait, in the game dwarves could have the "Has been forced to talk to somebody annoying/dangerous lately" just by having a hated attribute and in the event of a tantrum those dwarfs will be prioritised abode other as targets for assault/vandalism and if they have a important position everybody in the fortress would have a bad thought. Of course this can be solved by forcing interaction between these dwarves, having a outcast mayor that increases the quality of life of the fortress, creating an artifact and heroic acts can lead to a retrieval of the racism or even get into the "good" traits that the dwarfs want their children to have.
For thing like atheism there could be something like a "faith" percentage, heroic acts by faithful people would lead to the percentage to stay the same or even get higher if the act was particularly impressive but the passing of time and evil acts by faithful people would lead to a progressive atheism in the population. Churches and religious sites can slow down considerably the coming of the atheism and big events like wars and megabeasts can return the percentage to normal, they want to have something bigger than themselves to feel safe.