That would actualy be an interesting idea i admit, even if the connection to humanity would still be somewhat thin, once again making them "alien" characters so to speak, at least it would give them a chance to create their own idependent foundation and potentialy make readers interested in keeping as much of them around as possible, even after an extinction storyline.
Not to forget making readers care for them on a more personal level, than just the "epic" level we currently got so far.
It could even lead to a bit of a "stranger in a stranger world" storyline when some of these new characters would actualy be shown interacting with Earth and the Krakoan mutants, after the reader had enough time to get a feel for the Arraki mindset and what their "normal" is. Again creating care.
So yeah if that would be pulled out well, i could imagine many to be supporting for them not to be wiped out from the Marvel universe again and wanting to see them last at least in some capacity, even if they remain a "distant" part from the urban centric foundation of the mutants and X-men.