That annoyed me how in GalCiv 2, I could wipe out one race after another, yet still be officially "good".
I tend to believe that the result of conquering a planet isn't the mass execution of the populace, but rather the mass disenfranchisement of the populace. After all, it's stated that the listed planetary population is the number of your citizens on the planet, not necessarily the true planetary population.
This time, I think that would be neat if you could win Malevolence points for declaring an unjustified war against a innocent neighbor and conquering their planets.
Problem: define 'unjustified war.' Violations of claimed space and influence pushes are aggressive acts, and in my opinion I am within my rights to treat them as such. Setting up a colony in my back yard is also arguably a hostile action, as is building a space station of any kind in 'my' space (and worse, the game has an at best poor method of defining territorial space in influence). Declaring war to reclaim colonies lost in a previous war is also not necessarily malevolent.
Or, on the other side, maybe getting Benevolence points for intervening in a war that an evil race started (fighting in the war, ending it with diplomacy, or even just supporting the other side with credits/techs)
Problem: preventing a hostile empire from (quickly or cheaply) winning a war and becoming more powerful is pragmatic rather than strictly benevolent. Entering a war on the side of the weaker party to prevent their opponent from becoming more powerful is also pragmatic rather than strictly benevolent. Entering a war on the side of the weaker party so you can weaken the stronger party while they're distracted is at best pragmatic and could be malevolent. Ending the war without wiping out or reforming an evil empire (reforming as in improving the character of, not recreating, one) is more pragmatic than benevolent.
Pragmatism points if you bribe or manipulate yet another race into doing your dirty work against a rival.
This is arguably at least as malevolent as it is pragmatic, as if I can manipulate another faction into fighting a rival of mine, I can weaken two potential opponents and distract them, giving me an opportunity to go after them while they're busy, or after their allies while their forces are too thinly stretched to intervene effectively. Playing multiple factions off against one another to maintain a balance of power of some kind is at best pragmatic, if it's to keep any one rival from becoming too strong to fight, and could be malevolent, if it's to keep any potential rivals weak and divided.
helping your less developed neighbors catch up.
This is the one thing on your list which is most clearly benevolent. However, this can easily be a pragmatic action rather than a benevolent one, as a technologically backwards neighbor is not a very useful ally against anyone who isn't about as technologically backwards as they are.
The problem with assigning a moral judgment to any game actions is that it carries assumptions about why I'm doing something. Intervening to defend a trading partner so that my economy doesn't get too badly screwed up isn't really benevolent, nor is building up a potential ally's technological level. Causing two states to fight one another is pragmatic, in that it weakens potential rivals and targets at little direct cost, but it is also malevolent, especially if you're doing it to keep them busy while you go off and do something to the states that they might have aided had they not been busy or if you do it to distract them while you prepare to slip a knife into their back, or if you get them to declare war on an ally so that you can avoid the malevolent penalty for being honest about your wars of aggression while dragging your allies into the war despite the alliances being more like mutual defense pacts (here's a 100 BC, now go declare war on the Altarian Republic. Woops, I'm allied to the Altarians? Oh dear, I "didn't know" that. Well, I'll just help myself to these colonies over here, and smash a couple of your fleets over there, and ...).