Israel considers Gaza occupied territory. If the Turkish warship enters it's territorial waters and the Israelis intercept the cargo boat then this would quickly escalate, probably into one or the other committing an act of war. The Turks have been doing a lot of diplomatic and political talking and posturing, but little in the way of actual sabre rattling. It's not long ago Turkey and Israel were allies - this would be a massive, massive reversal of that and a huge risk for them. As far as I can tell (as the real story is not clear and more than a little confused), the Turkish government made the flotilla organisers change the flag of the Mavi Marmara to another country (Comoros) at the last minute to avoid just this sort of situation developing. I think the best they would do is escort the vessel through international waters. Turkey enjoys the automatic protection of NATO if they were attacked, but not if they were considered in any way the aggressor, which would quickly be used by the NATO allies as a get out clause.