If humans and mutants could truly be separated by living on different planets then that might be the way to go. But even if every mutant alive right now lived on Mars or some other planet, humans would continue to give birth to mutants, and those mutants would suffer the same persecution. Krakoa provides a possible safe haven for such mutants as well as a political shield since they can act in defense of mutants everywhere. An entirely different planet is far less appealing as a safe haven for mutants who grew up in suburbia and will not be able to act on behalf of the mutants still on earth as a nation that's a part of earth can.

Arrako was a unique case since they were culturally incapable of living in harmony with humans in a way that even the likes of Magneto and Apocalypse are not. They are also newcomers to earth and so don't have strong feelings or ties towards the blue planet.