With a time machine, I guess the C'tan could just go and kill all the humans specifically. They saw them as only tree-swinging feral, non-sentient dumb animals, another of the Old Ones little creations that was doing them no good.
Of course, they could've easily targeted and erased them. Then there would've been no human race, no Emperor, no Imperium.... no Chaos Gods (damn emotions of yours) no problems, no nothing!!!!
I HAVE THE ANSWER!
EDIT: In the mean time, I better go and help silly Serp....hmmmm....
Oh, and also, EH, is the Outsider doing nothing? Surely he'd help us, and he's just been freed; I doubt he can contain himself from eating some humans.
Give a man a match, and he's warm for a day.
Set a man on fire, and he's warm for the rest of his life!