It didn't seem plausible that every single colonist could have evacuated in time to escape Sisko's wmd. How many thousands of colonists were there anyway? What about the Maquis children?



From what was shown, the wmd started to effect the biosphere immediately.
Sisko demonstrated in "In the Pale Moonlight" that he could lie and cover up his crimes and illegalities like any politician. Sisko essentially believed that the ends justified the means that he used to bring the Romulans into the war. Disinformation, accessory to murder, bribery and ultimately the cover up.
For Sisko, it seemed like an ends justified the means situation regarding his handling of the Maquis as well.
Because Sisko seemed to hate the Maquis with the same passion as his wanting to bring the Romulans into the war, it wouldn't be farfetched to believe that Sisko would lie and cover up the actual effects of his wmd against the Maquis colonists or anything else concerning the Maquis.