how about Necrons and Sisters of Battle, those two are at war as well, wherever Necrons pop out, Sisters of battle soon follow to purge the undead. Aside from Soulstorm, I haven't seen anything about the Sisters of battle even though they are a great branch of Emperor's army.
What? No no no...
Sisters of battle are a militant arm of the church and are unofficial warriors of Ordo Hereticus, which is rooting dangers from within the Imperium. Do you know what that means? That means that most of the killings Sisters of Battle do, is humans who are not loyal to the Imperium and more importantly not loyal to the church (heretics).
The part of the Inquisition that specializes in Xeno Purge is Ordo Xenos and they employ Deathwatch, not Sisters of Battle. I have no idea from where you got the idea that Sisters of Battle hunt Necrons.
Actually the only race dedicated to hunting down Necrons is the Eldar, since they were created by the Old ones for one purpose only: to battle the Necrontyr. Hell, even in Dawn of War games you see Eldar appearing in campaign as a response to Necrons waking up.
There are also Tau that have't yet had much fun in games, I was hoping for at least the Tau empire to hit in DOW2 so I could play some in The Last Stand.
Meh, everyone knows that Tau was a lame attempt to market Warhammer 40K game in Japan and other Asian countries around it. Hence the reason why Tau have that mecha exosuits

Still waiting for the release over here....