First off, let's lose the 2 point morality system, as despite 40k's strong focus on the Chaos/Purity scale, that's not all there is, and some things don't really make sense with regards to it. I'd suggest a 4 point scale. You have the standard Corruption/Faith, which represents falling/dealing with Chaos, or rising above it's influence/staying true to the emperor.

Then you have another scale, which needs descriptors, but involves choices that aren't dealing with Laws and Social Mores. This is where stuff like temporary Xenos alliances would fall.