I read the issue as the Krakoa stealing the magic of Avalon to create mutant magic.That is why Morgan wants to destroy the mutants. The metaphor of mutant taking resources from the normal people has always been present. In fact we know krakoa kills slowly other plants as we have seen un new mutants. The theme of competition is prevalent in Dawn of X.
The endgame would be Krakoa growing over all the planet and all no mutant life destroyed