Thus, despite the bitter conflict with those Hellenistic rulers who sought to accommodate it forcibly to the customs and idolatrous cult of the Greeks, biblical faith, in the Hellenistic period, encountered the best of Greek thought at a deep level, resulting in a mutual enrichment evident especially in the later wisdom literature.
According to Maccabees I (which is part of the Greek Jewish bible, the Septuagiant, and then the Catholic Apocryphah), the Greek ruler of one of the successor kingdoms to the empire of Alexander the Great, Antiochus IV Epiphanes attempted to suppress the Jewish religion in the second century B.C. This inspired the revolt the successful revolt by the Maccabees and the establishment of a Jewish state. A miraculous version of these events is commemorated in Hannukah, which we goyim know about because the multicultural state used it as the first winter solstice celebration used to make the "Christmas season" more inclusive, notwithstanding its relative lack of importance in the Jewish tradition. (This kind of ecumenism is satirized by Jon Lovitz's Hannukah Harry, who constantly saves Christmas from evildoers).
I suspect that Benedict was trying to signal that the Greek tradition of respect for reason and dialectic did not always translate into practical tolerance. The norm of religious tolerance and rational persuasion dialectically derives from the Greek tradition - it did not at all times and in all places characterize it.
We all might have liked him to use some Christian examples, as well, but I think he was implying that the Inquisition or the Conquistadors were the successors of Antiochus, which is not a compliment.