I was convinced that Moriarty was Irene's puppet after the S1 finale, where Sherlock went around saying things like "This whole case has a Bohemian feel," but am less convinced now after "Scandal in Belgravia". Though I did read her mention of Moriarty in the airplane scene as implying that yes, she was the one who'd hired Moriarty to harass Holmes in the finale, I'm not sure that this interpretation is actually what they wanted us to extract from that mention.