In this passage the final occurrence of the pronoun it is redundant. Without the two intervening subordinate clauses (“when it is fully ripe” and “if the wind bloweth”), the clause-initial relative pronoun which would be sufficient: “thou shalt be as the blossoms of a thistle which is driven forth upon the face of the land”. But given the intervening subordinate clauses, the redundant it refers the reader back to the thistle mentioned near the beginning of the sentence, thus helping the reader process the complex syntax of the entire sentence. Note especially that in the second subordinate clause (“if the wind bloweth”) the subject switches from the preceding it (referring to a thistle) to the wind, thus virtually forcing the repetition of the pronoun it. The critical text will, of course, retain this redundant usage.
Summary: Maintain the redundant use of it in Mosiah 12:12 (“which when it is fully ripe if the wind bloweth / it is driven forth upon the face of the land”).