Here it refers back to the whole sentence before it, or to the idea, "any man's doing wrong merely out of ill nature."
(3) As a grammatical subject, to stand for the real, logical subject, which follows the verb; as in the sentences,—
It is easy in the world to live after the world's opinion. —Emerson.
It is this haziness of intellectual vision which is the malady of all classes of men by nature.—Newman.
It is a pity that he has so much learning, or that he has not a great deal more.—Addison.
(4) As an impersonal subject in certain expressions which need no other subject; as,—
It is finger-cold, and prudent farmers get in their barreled apples.—Thoreau.
And when I awoke, it rained.—Coleridge.
For when it dawned, they dropped their arms.—Id.
It was late and after midnight.—De Quincey.