Right, because "chief" Rabbi Yonah Metzger runs Israel.
I'm aware of their proximity and pragmatic reasoning for strengthening ties between the nations, but at the very least, an Orthodox Archbishop who wields considerable power and theoretically represents the Orthodox Church, calling for closer ties (the article gave no real information on what that meant) with a representative of a portion of Jews in Israel is a bit odd.
If Archbishop Chrysostomos II wanted to meet with the P.M. or Foreign Minister (note that he's met with President Medvedev), that would be a different story. If Christofias wanted to meet? Even more normal. So were they discussing religion or not?
Edit to add: Claiming this is odd is not the same as claiming it is unexpected or illogical. Yet another reason why I dislike mixing of church and state.