My answer is
(C). It took me 03:33. I had to run five options twice, and then weighed between (C) and (E).
First pass(A) It is nonsensical / comical to claim that "apple growers" were "(b)elieved once to be essential in preventing crop destruction".
(B) "they" in "they were identified" naturally refers to "Apple growers", but readers then realize "they" refers to "certain pesticides". So "they" does not have a clear antecedent, to say the least.
The use of "and" does not convey the cause-and-effect relationship between two clauses clearly.
Also, the use of a noun (prevention) is not as active / concise as the use of a verb ("prevent"), as (A) does.
(C) "them" can refer to "Apple growers" or "certain pesticides". Such ambiguity cannot be easily disambiguated as readers are likely to believe that "them" refers to "Apple growers".
Also, the use of a noun (prevention) is not as active / concise as the use of a verb ("prevent"), as (A) does.
(D) How to account for "it was once believed"? It sounds ok. I just treated it as a nonessential parenthesis.
It is wrong to suggest that "apple growers" are "essential in preventing crop destruction”
(E) In the first pass, I eliminated (E) mainly because it seems that the antecedent for "that" in "that have been identified" is "apple growers". More analysis below.
So I eliminated all five options! Have to loosen the standard and review them a second time.
Second passI had to go through all five options again because I had no paper trail of the though process in the first pass.
I narrowed the field down to between (C) and (E).
Option (C)The ambiguity of the antecedent for "them" is disturbing but may not be fatal.
The use of "prevention" instead of "prevent" is a minor issue.
The relationship denotated by "because" is logical and effective.
The use of active voice throughout the sentence ("decreased the use" and "identified them") is a plus.
Option (E)"apple growers" are people, so "that" in "that have been identified" cannot actually refer to "apple growers". It is actually possible that "that" refers to "certain pesticides" then.
Still, the distance between "certain pesticides" and "that" makes such connection rather tenuous.
Can we say "the use of certain pesticide", rather than "certain pesticide", was once believed to be "essential in the prevention of crop destruction"? I think it is ok.
Note the use of of "prevention" instead of "prevent". No advantage here over (C).
The consistent use of passive voice ("been decreased" and "been identified") is not as effective as active voice in (C).
The relationship between "been decreased" and "been identified" is not explicitly revealed.
Ultimately, I found that (E) contains more issues to be an effective sentence. (C) is not without issues (and does cause misreading) but is still a better sentence.