on the farm / in the farm?

You are correct in saying that "one" is a pronoun which replaces "a farm" in the sentence and "in which" is also a relative pronoun which refers to 'a farm'. Your question is very reasonable but the answer is quite complex. First of all, the word 'farm' (as a noun) can refer to the whole of the property - the land, fields, buildings and the farmhouse itself - or just the farmhouse or just the operation of farming in general (without any reference to a specific farm). 'On' is probably the most common preposition but 'in' might occasionally be used to mean 'within the boundaries of the farm' or, as here, where Rachel Carson is referring to a farming practice rather than a physical entity. It would be grammatically correct to say, for example: "In a farm where wheat is intermingled with other crops, an insect which lives solely on wheat cannot build up its population to such high levels." because 'farm' here refers more to a farming practice or method than to any specific (or general) physical area. Another reason why the writer may have chosen 'in which' rather than 'on which' is because the phrase "... than on one on which wheat ..." simply sounds awkward and confusing.

Heh. I'm glad somebody was able to explain this well. I ended up getting confused myself.