Choice D is the best answer. Passage 2 begins with Thoreau's statement that "unjust laws exist" (line 45,"Unjust...exist"). His philosophy regarding how to deal with those unjust laws is evident in lines 58-59("If the injustice... let it go"): "If the injustice is part of the necessary friction of the machine of government, let it go, let it go." Thoreau believes, in other words, that some injustices are an unfortunate part of normal governance and just need to be endured ("let it go, let it go").
Choice A is incorrect because Thoreau does not say some unjust aspects of government can be fixed easily or that they are merely superficial. Choice B is incorrect because Thoreau does not argue that such injustices are subtle and should be studied, but rather that in certain cases it is best to "let it go, let it go" (line 59), while in other cases one should act or "break the law" (line 66). Choice C is incorrect because Thoreau does not say that any such unjust aspects of government are beneficial or helpful.