Just an amateur here, no claim to expert knowledge, but I think the "who" is correct. I limit my use of "whom" to situations where it is the object of a preposition, "for whom the bell tolls." So then the following two sentences would be correct (spoken to someone approaching a desk for information): "Who did you wish to see?", "To whom did you wish to speak?", or more awkwardly, "Whom did you wish to speak to?" So see who, speak to whom. In the given sentence, "she supposed it was he," is just as good as, "she supposed it was him," perhaps better, so I don't think that gives a clue to the who/whom selection. The same problem occurs with the subject/object analysis, is her brother the subject of Anne's suspicion, making it whom under the rules, or is the brother the subject of the prepositional phrase, "of her brother," to which the following phrase refers, making it "who"? I don't think it's clear, so that doesn't help, either. Only the lack of a preposition makes me go with "who".