As someone said before about using Culture spread - it's called making a tough decision and sticking to it.
This reminds me of how people whined that in Fable (I've never played that game actually) if you chose the "good" path you ended up scarred and whatever and cried about how being good should have a better reward than being bad...
Guess what? Being good is NOT the easy path. The path of the "dark side" is the easy path of anger and violence.
Being a "Good Guy" means:
Knowing that for every evil you stop there is a hundred more being commited and a hundred more will be born from your acts of "goodness" that others take offense to and become villains because of you.
- "The Crimson Chin" gives Timmy Turner (From Fairly Odd Parents) a lecture on how he as a crime fighter (The Masked Magician) will one day create a villain trying to stop evil. I think there was a speech by Bruce Wayne to Terry in "Batman Beyond" along these lines as well.
Being a "Good Guy" means:
Thinking of others above yourself and above your own life.
It means giving up little pieces of yourself day after day until your hollowed out shell either needs to retire in peace or becomes filled with the evil you have spent your whole life fighting.
To sum up:
We have a mechanic to take a planet bloodlessly -Culture- and it is the tough road to only engage the military units and win by converting the populace but that's what it means to be a "Good Guy".
PS I love the (I believe Advent) Cap ship ability "Hysteria" where you hear the whole planet screaming with skulls popping up here and there as the people rebel and kill each other and pillage and loot in an extinction panic.