I agree that such immersion would be a good thing, but to make it work, you'd almost have to build the game around it, and I'd say it's a bit too late for that with GC3.
Although, this can maybe be done a bit less directly. Say, maybe Benevolent doesn't lose points for declaring war and such, but gets an invasion penalty, and a temporary moral loss upon declarations of war (Strategic benevolent players will simply provoke other civs, but will have to do so by means other than sending warships into enemy territory to avoid the moral loss). They get 2X the planetary defense boost, though, to make the alignment more desirable(wars can't be won defensively, so it'd almost have to be boosted by double). Malevolent, rather than being the inverse, has a different problem. They may not have to conquer to win, but can face revolts for playing too defensively while in the midst of a war, they'll get a warning before it starts happening, and has to be more than 50-60% of the fights happening in their space(and not near any borders) and their planets before they are at risk, but they still have make sure to be somewhat agressive, lest they lose planets to a new civ that is instantly at war with them.
Pragmatic, naturally faces no penalty for any playstyle, at least not domestically. Being neutral during wars can carry its own diplomatic risks if you're already seen as a pragmatist. They may not get war declared on them for this alone, but it becomes more likely to happen, especially if they trade with civs on both sides of the conflict.
So it can still be done, at least sort of, without constraining player choices. Not on the level of a game built around it, but enough to add flavor and complexity.