Board Thread:Warhammer 40k General Discussion/@comment-14745711-20140911102114/@comment-25073042-20140919072416

As it is clearly stated in the "Long War" page on this wiki:

"The Long War is a term used by Chaos Space Marines of the Traitor Legions andRenegade Space Marine warbands to refer to their fight to overthrow the Emperor of Mankind and seize control of the Imperium of Man for themselves and for the Chaos Gods."

So to me this means that the gods send their champions (like Horus or Abaddon) to take control of Humanity, not destroy it. And as far as I can see, Humanity is the only faction in the galaxy, the gods make an effort of controlling. So even if they can survive without it, they just don't want to destroy it. So sending someone back in time to take out emps and therefore humanity is out of the question.

And besides, maybe they enjoy the Long War as a form of entertainment? And that's why they don't actually want to end it.