While true the papacy began closing churches which used the Greek rite within southern Italy I think more of the blame should be leveled against the Legate Humbert for resorting to an excommunication that at the time he did not have the authority to offer.
The Pope and the Ecumenical Patriarch were both under the shadows of their own respective emperors and while Pope Leo IX was a reforming pope and supported the idea of a papal monarchy over Western Christendom the reality was that he still was under the Emperor of the HRE.