This short guide contains few useful tips to protect from poison.
Guide to Protect from Poison
Currently the easiest way (if you know the trick, it’s way too easy) is to pause the game after the cloud has spawned the plants, and then issue harvest commands for all of the poisoned plants with a priority set to high.
If you disable other buildings to have enough free workers, the spores should be removed very very quickly.
Keep a doctor ready with herbs, because it poisons your workers.
You should pull out your workers of non food related and doctor jobs to remove the plants.
Wood/stone/mushrooms/onbu food/ catapult/scavengers: not important before a cloud.
If you wait for too long, the spores spread exponentially, which makes it impossible to contain after a while.