Couldn't the Dunmer have just chiseled the meteorite to nothing after Vivec disappeared while it was still held up by the Ingenium? It's not like it would take a long time or that the meteor was invulnerable. The Dunmer did hollow it out to make the Ministry of Truth, what stopped them from simply hacking it to tiny pieces with pickaxes?

I doubt that the Dunmer at large knew anything about the Ingenium (haven't read the novels, sorry), and would have refused to destroy the rock on religious grounds. The Ministry of Truth was a divine artifact as far as they're concerned. Even though Vivec had disappeared, he had become more shut-in before that point, and the rock was a proof of his power (even if it wasn't his). Also, there were only 11 years between the fulfillment of the Nerevarine Prophecies and the Red Year. If Lie Rock was much bigger than we see in the game, then it could have taken at least that long.

This isn't so much a plot hole, as it's just a matter of the way things turned out. Stranger things have happened.

I think the moon is supposed to be far larger than it is portrayed in-game. At its current size it would barely destroy the Temple district of Vivec, let alone the entire country.