From the Jerusalem Post:
"Deputy Foreign Minister Danny Ayalon said unequivocally on Sunday that Israel had no intention of apologizing, and one diplomatic source said Thursday there were voices inside the government saying that not only should Israel not apologize, but it should demand a Turkish apology for facilitating the dispatch of a ship with terrorist supporters who beat Israeli soldiers trying to protect its territorial sovereignty."
So, a ship carrying aid to Gaza had to be stopped to protect Israel's territorial sovereignty. No further analysis required.