What I'm suggesting is that survivors from a Lunar/Martian colony (using whatever they had left from the Conestoga project), managed to carve out some kind of space faring civilization in the years that the Conestoga was drifting. It will be difficult, sure, but if the technology seen in Eden (The first colony), is any indication then I think it's entirely possible for 'earth survivors', taking copies of the devices used on the conestoga, to move to Mars or the moon and create an outpost there.
They wouldn't need the same resources the Conestoga (or New Terra emigration ship) because they aren't leaving the solar system- just going to another planet in a separate orbit.
From there, while the Conestoga was still in flight, humanity would be looking to either build another starship for complete evacuation of the solar system... or establishing a new civilization on a different planet. Either way, I like to think the possibility is open for human survival in the solar system if they were able to construct an interstellar spacecraft.
Come 100 years after Earth's been wiped out, I would imagine that interstellar probes would have been launched from the new solar colonies to explore the universe... find other planets for colonization... or in the very least find the Conestoga and see if they had better luck than the martian/lunar colony.
And what do people say to the idea of the other colony going to new Terra's moon and building a base there? Are we to assume that the moon of this world has no usable resources at all?