My context isn't about conflict, but maybe I can help a little.
'There are rarely two clear cut sides in human conflict'
Do you feel that this is true? You said good and evil, but surely you can agree that there's more to it? For starters, which side is to be considered good or evil? The 'evil' side considers themselves to be 'good', as do the 'good' side. Then there's also the gradient of individuals and groups in the middle, are they fighting together because of a common enemy? Do they have other motives? Did they choose to be a participant in the conflict or were they forced to participate?
Take the Russian Civil War, there was a collective of armies known as the 'White Armies' trying to overthrow the Bolshevik Government. But very few, if any even, of these armies collaborated together, it's all very well to group them together under the label of 'White'. But does this label truly encompass their side? One of these white armies (Mensheviks iirc) wanted to start their own separate Socialist Republic, but then another one came and wiped them out.
In this example, it's their motivations that distinguish them from one another, despite sharing a similar goal (Remove the Bolsheviks from power), they had their own separate motivations and aspirations. One wanted to see the system of Tsarism reinstated, whilst the other wanted to be in control themselves. And so you see, there really is no clear 'White side'. Each participant in the Civil War had their own agendas they wished to see fulfilled, and each had their own methods of attempting to do this.
Hopefully that helps you.