It seems that the real disaster was a later event. Lucasfilm's Lore Advisor Pablo Hidalgo, while not speaking on behalf of the showrunners, says this:
I think the disaster that finally closes up shop happened afterwards if it’s attributed to the Empire.
The starwars.com Episode Guide for Episode 2 says that as of the flashback, Kenari has "ruins" from "massive mining operations", but not that it's uninhabitable:
In the past, a young Cassian Andor -- or Kassa -- and his tribe traverse the wilderness of Kenari, surveying the ruins of a world with deep scars from massive mining operations.
(source: https://www.starwars.com/series/andor/andor-season-1-episode-2-episode-guide, Story Gallery image 1)
This is corroborated by the Episode Guide for Episode 3:
The flashbacks in this episode occur during the later years of the Republic, prior to the start of the Clone Wars, with Maarva and Clem worrying about an incoming Republic frigate interrupting their salvage operation. The dead crewers aboard the transport corsair wear uniforms with a symbol closely related to the eventual Separatist Alliance. Travel to Kenari will later be restricted by the Empire due to environmental disaster.
(source: https://www.starwars.com/series/andor/andor-season-1-episode-3-episode-guide, Trivia Gallery image 1, emphasis added)