The log entry just said colonists switched planets. It didn't say anything about percentages or anything and the whole tone of the log entry sounded like Sisko was just covering his ass on that one to justify things.
He gave them an hour... they thought he was bluffing and did nothing and didn't start evacuating until -after- Sisko fired a weapon of mass destruction on them. Jail time for that alone, regardless of if people died or not. Which is naive to assume they didn't given Picard was crying over how unstable the trilithium stuff was for a whole episode in TNG and it was the same stuff Soran used to blow up a star in Generations. The stuff kills and it spread across the planet almost instantaneously by that graphic of the planet turning yellow.
So yeah... you have a deadly compound spread across the planet and you think everyone on the planet, however many there are, however spread out they are, is instantly going to be notified somehow and to get into a ship to escape on a few minutes notice, because of course a group of terrorists is so well equipped that having enough equipment is never an issue. That's bending the arm of coincidence to say the least.