I think your right for instance a Benevolent society should have a major Morale issue if they start a war or use weapons of max distruction on planets, etc. While Malevolent society should suffer morale penalties for maintaining peacful relations with another civilization.
A pragmatic culture would have neither type of peanalty and to balance this maybe there should also be benefits like a Malevolent society getting a Morale boost for conquering planets and starting wars and a Benevolent society getting a boost from agreeing alliances and peace treaties.
I also don't like that in the current system you can be all three at once, rather than being forced to choose a path although if they didn't allow that it would mean that Colonization Events wouldn't be so interesting I admit.
So in terms of the bonus and penalty system I suggest your peoples ideology would be whichever ideology you currently had the most points in.