Willed out of existence.
There you go.
Seriously, y'all aint getting how broken mahvel is.
That's the thing.
The Warp and the Chaos that live in it can't be willed out of existence. The warp is compromised over everything that created the universe and living creatures, which the Chaos Gods have dominion over. Every action serves to only strengthen the Chaos Gods.
Let's talk about Richard Franklins. His power is to literally change things to how he see fits. Tzeentch feeds off that-and in turn he becomes stronger than Franklin Richards, and the Warp changes and molds into something that will only feed off Franklin Richards. It'll be that shadow in his eye, where even if he thinks he extinguishes it, it'll simply be looming in his new reality.
You can't really kill or wish away a Chaos God. Again, Tzeentch for example. If for whatever reason the Marvel Universe touched the W40K universe, then Tzeentch has known about it. His intelligence and power is such that it would probably be revealed that all the magic in the Marvel Universe came from Tzeentches machinations from millenia ago. So how do you stop Tzeentch? You stop wanting change. You stop hoping. You stop being afraid of the future. He is literally fed off the act of wanting change, of wanting to see what tomorrow holds, of being afraid, of wanting knowledge, etc. Everyone and everything that has emotions or thoughts like that inadvertently feeds Tzeentch-The more strong-willed people feed him more than someone weak, and it all serves to increase his dominion over the Warp. It's why the Chaos gods fight constantly-If ones dominion over the Warp becomes too strong, then they start bending reality to their will.
Khorne feeds off violence and bloodshed. As long as you have your super heroes killing or destroying, then he'll be fed in power at a magnitude greater than what the super heroes output. Galactus destroys a planet? Khorne is that much stronger. A whole galaxy is wiped out? Than Khorne is that much stronger.
Slaanesh feeds off desires and lust. Even the strongest knight couldn't strike him down when Slaanesh took the form of a pure, beautiful, young androgynous child. One look at him, and he'll have you in his palm immediately.
Nurgle feeds of death. Even if the heroes killed off every invader possible, then Nurgle gets that much stronger. Everyone who's ever been sick has felt his touch already. As such in the back of your minds, you feel Nurgle-many people who know about the Chaos gods in the W40K universe know that when they die they'll simply go over to Nurgle.
No Marvel hero can simply 'wish' them away-because that would be eliminating the Warp, and if the Warp acts the same in the W40K universe, then the second it touches the Marvel universe, the Warp becomes part of it's universe and it becomes necessary in order to continue existing. As long as Marvel super heroes have basic emotions, then the Chaos Gods will continue to be fed and grow stronger. That is the reality of the Warp. Even if a situation arised where Marvel pushed back the warp into it's proper universe, than the Marvel Universe would continue to be tainted by the presence of the Chaos Gods, simply because they affect everything and everyone as long as those people continue to dream, hope, lust, war amongst each other, and die.