Krakoa has superpowers and alien alies, they have 0 necessity for humans, every bit of shiar tech surpasses anything humans can provide and they are more trustworthy , you have no garantee any human that is "alligned" with krakoa isnt actually a spy or a new type of anti mutant weapon, it be an immensly stupid move.
Mutants can easly even completly leave earth once their population is self sufficient, mars and the shiar empire are much better alternatives than earth and humanity, it has been proven time and time again.
Hell it even seems krakoa manages to get along with the kree-skrull alliance.