What’s the deal?
First of all, one has to distinguish between the corporate position of the Holy See and the personal position of Joseph Ratzinger. In fact, there has been no real change at all in the former. Vatican diplomats have always said that they are officially neutral on the question of Turkey’s admission, but that if Turkey is to join the EU, it should be required to meet European standards of human rights, the so-called “Copenhagen criteria,” especially with regard to religious freedom.
As far as Ratzinger personally is concerned, Donohue has a point that he has not flip-flopped,” because that would suggest a 180-degree reversal from firm opposition to clear support. That’s not the situation. Instead, he’s moved from opposition to something like a “yellow light,” meaning that he’s open to Turkey’s candidacy in principle, but with conditions, especially what the Vatican calls "reciprocity,” meaning guarantees of religious liberty.
His earlier opposition is not in doubt.
Background info- from Sandro Magister: (10-15-2004) Europe Is Christian, but Turkey's Crescent Moon Shines in its Skies.