Your quit right, repopulating would take quite a long time. So much of the planet would be empty.
As with most population distributions, certain areas would be populated first, and others left until later. This would allow the player to visit the cities on occasion, whilst still managing to spend a significant amount of time in isolation.
As for having a Cocytian as part of your group, for some of the game, I think that's a good idea.
As for getting the guys back on Cocytus, one of the aliens could bring them back, because the civilization is in trouble, and the alien knows how they helped the Cocytians get back from Space Time 6. The cocytian in the group could either be that particular alien or his protege etc.
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