Ghostwriter

As you said, it would be chaos.
The ship was already packed with more citizens than it could safely carry, and the sudden hole as the cardboard vessel breached the ship would throw the already unbalanced ship further off tilt.
The crew had enough trouble as it was keeping the ship on course, they would have no time to deal with the hole created.
The ship would still reach the station, but it would be a rough landing.

On the station, there would be a steady trickle of lizard people boarding spacecraft to head home. The stations resources were already being strained to the limits from the refugees, and it was clear that it would take time for the lizard people homeworlds to send aid. Already high tension would begin to raise further, threatening to boil over at any time.

Meanwhile, a vessel sent by the refugians would continue its journey through space, utterly unawares of the events on chiron following the beacon. There would be a lingering concern over the communication silence, the beacon sending only the one message. Concern over who was out there to find and use the beacon. An uncomfortable awareness that it was a very, very long time ago that the only prior vessel to visit chiron was an unmanned drone.

SpoilerShow

It's difficult to say what the endgame should be.
From the scope of this story, the natural endpoint would be after our characters survive the apocalypse, and find a firm footing once more. The end of book one, as it were.

But were the story to instead continue into book two, there is plenty of room for a story of tension between the tripod refugees and the lizard people.
And of course the refugians arrival at the end of THIS story would make for a workable cliffhanger.
I suppose then it might be a matter of if we need our current characters to partake in book two.
With their survival handled, we could pluck them from the end of book one easily enough.
And if needed, could come back to the setting in the future. As a whole it seems stable enough that with a bit of care, it could produce ghosts for quite some time.