The answer to your question would be that the verb that should be used with the helping verb "had" in the sentence is the following one: frozen. That is, the sentence would be as follows "despite the grove owners' hard work, the orange crop had frozen overnight.
The auxiliary verb "have" in the past indicates that the following verb should be in the past participle form for the sentence to be in the past perfect tense. The past participle of the verb "to freeze" is "frozen".