It's simple physics, everything decays given enough time. Sure that time could be billions upon billions of years, but it will still happen. Given a sufficient period of time any act, however improbable, can be considered guaranteed. The death of the C'tan is highly improbable so clearly it will require a very long period of time to be considered guaranteed, but it will still happen.
How can you claim this as a certainty? The c'tan are cited as being tied to the very fabric of the universe and therefore nigh impossible to destroy. I could argue that their death won't occur until the universe itself finally collapses because there is no naturally occurring phenomenon capable of ending their existence.
My question again would be: is that a loss? I don't think we can say that losing influence over the material realm is something that Chaos would be overly concerned with.
Well it certainly isn't a lasting victory over the materium is it?