I'm going to guess tentatively that no one who evacuated Krakoa has actually died, and that the cliffhanger’s resolution will be that Darwin and/or Warlock redirected the gates to a safe location. And that wherever everyone went, it's just too far out of Xavier's range for him to detect. I think that would be a good way to pay off Darwin becoming one with Cerebro--and promising Forge it would help everyone later on--and with Warlock surviving on inside of the machines to help his friends.
That Destiny thought it was the right call to accept exile and fight another day, and was so sure that Manifold had the ability to save everyone, tells me that they weren't all just marching to their deaths under Xavier's control. They’re somewhere in a real place, where Eden will still be able to discover them. I think also that all of the set-up we’ve had so far has been oriented around the idea that the mutants (and ordinary humans tbh) are in dire straits, but that they haven’t lost yet. We also already know that Magik, Mirage, and Mary made it out alive to star in their own book in Otherworld, though I guess it's not really clear if everyone else is with them or if the survivors have all been split up.
(It’s also possible that Stasis and Moira just actually kept their word and let everyone escape to somewhere the X-Men can’t reach, but I don’t think so since Duggan is the event’s lead writer and he’s leaned so hard into the idea that the mutants vs machines war only persists because Orchis are lying genocidal maniacs.)