I assume time corrects for anything Rory did.
anyways I am not 100% convinced we wont see him again, on that note they seemed to do too much set up, for the Doctor & Amy not to visit the Silurians again in 1,000 years time.
Talking of I enjoyed the Silurian plot, and the fact that they were more individuals than previous Who aliens, who have all tended to look exactly alike.
Since we dont know what caused the cracks, we can speculate across, but it seems hard to say what has and what hasnt been sucked into the crack.
Any reason why the female of the Silurians seemed to be the warrior type? seemed odd.