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Yes, the freighter people want the island in a non-gassed state. They wanted to disable the gas so that Ben couldn't use it against the other freighter people when they showed up with machine guns. The freighter people didn't want to use the gas to accomplish their mission for some reason - they'd rather shoot people up. Perhaps they are looking for something and the gas masks are very inconvenient to wear all the time until the gas dissipates. Besides, perhaps they have a list (like Ben) of who they want to keep alive. The gassing is indiscriminate and would kill everyone while with bullets they can choose who they want to kill.