Also, Sisko only fired two torpedoes, and fairly close together too, exploded into the upper atmosphere. That would take days, at least, to affect the whole planet (the way the green stuff spread was completely weird). Sure, he might have dropped them right on top of the colony, but it would still take time to fall. Scanners indicated that transports were scrambling after the attack; they obviously had some time to prepare (I'd bet that they were always on a short notice for evacuation, in case of Cardassian attack).
Yeah I'd point out they probably had some ships around in case they needed to evacuate due to a Cardassian attack, but the way that the chemical was spreading was quite rapid, and if this was a developed colony, and not just concentrated refugee camp, it would be extremely difficult for the Maquis to have ships around any human settlement, from homesteads to cities.
More importantly, Sisko never actually scans the colony to make sure. He heads towards the nearly colony, gives the warning, scans to see if the Maquis react, and then fires. He never scans to make sure there are enough cargo ships to evacuate the planet, or that the ships on the planet are in range of all humans on the planet before the weapon kills them.
Considering how rapidly the Maquis colony started evacuating, I'm not sure if these weapons would take days to reach human settlements.