One of the other basic reasons for allergies has been the the genetic modification of crops. They not only brought in pests as in the case of BT cotton fields but also changed the whole natural cycles around destroying the natural flora and fauna.
As Kalyani said our ancestors only used natural methods to grow crops and to destroy pests.
The other thing they did was to allow the soil to rest and replenish itself, like she pointed out they allowed cattle to graze and naturally nourish the soil with their waste. Today we have crop after crop and the soil is denuded of all nutrients and we have to resort to chemicals to grow them faster.