Quote Originally Posted by Malrubius
It should be that only selfless generals get pangs of conscience for exterminating populations (Restless Sleeper trait). It should take at least 3 exterminations before this occurs.

There are also 3 levels of selflessness (which are hidden from the player--you don't know exactly how smart or charismatic or loyal your general is naturally, but you have a general idea, and can discern more by watching his performance over time), and the chances are different for each level.
I hardly ever exterminate populations, but the damt Aitolians deserved it . My Mak general got the trait from that one time though (I'm sure it was just one time). He is unselfish/optimistic/loyal though.