The original sentence is correct. " The "but" overturns the "not" in the first part of the sentence, so that the second part of the sentence is no longer in the negative. Your revised sentence is correct, but it lacks the spirit of the original sentence.
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Debpriya De"This is not caused by evil, but by simple ignorance."I understand your reasoning, but the rephrasing is not necessary. We intuitively understand which words are missing in a way that makes the structures parallel.
Shouldn't we rephrase this sentence as "This is caused not by evil, but by ignorance" to make it grammatically correct