I was in Istanbul, Turkey earlier this month and happened on the MV Mavi Marmara at a dock in the Golden Horn (my pictures).
According to what information I can find, including several Turkish sources, the vessel is still registered in the Comoros Islands. That may be, but the Turkish flag has been reapplied to the side of the ship, and the vessel was flying the Turkish flag from the stern when I saw it in the Golden Horn. During the confrontation with the Israelis in 2010, the ship did not have the Turkish flag painted on the side, although there were huge Turkish cloth flags adorning the vessel. It also flew the Cormoros flag on the stern.
Most of the Turks I spoke with about this incident believe that the IHH activists were looking for a fight. They aslo expressed surprise that the Israelis took the bait and, in their view, overreacted. I tend to agree with that assessment, but then, it's always easy to second guess these things after the fact.