Not entirely. While less ambiguous than other games, it still is less black & white than 90% of games. For example, the Empire - or at least its subjects - are sometimes shown in almost-sympathetic way - especially the conscripted soldiers sent down to infiltrate The Pit. There is also some humanization of the Sliths and Nephilim, of whom you basically commit genocide of. I remember a Nephil slave that you release later on in the game who mentions intent of returning to her mate who lives in a Nephil fort which you, uh, kind of burned down to the ground earlier.
Edit: Talking about AEftP only - haven't played 2-6