Keep in mind, back when the first flotilla sailed, Turkey and Israel were still allies and the best of friends. Turkish authorities inspected those ships, and Israel still insisted on boarding them. They could have just let them reach Gaza, to be honest, and no harm would have been done but then the rightist government would have looked weak to their constituents. Since their entire platform rests on xenophobia and acting tough on Muslims, that wouldn't do.
The US should stay the hell out of it. Part of the reason why the entire world is going to recognize Palestine this month is that they can see that the Israeli government's insistence on having more and more settlements and preventing a reasonable peace deal from ever being reached is the primary problem in the peace process. If Obama had some nuts, he'd tell Netanyahu he's stuck fighting his own battles on all fronts (whether it's Turkey, the iffy relations with Egypt, and the demographic doom he's clinging to in the West Bank) until he starts behaving like an adult. Hell, it worked for Bush 1, of all presidents.
In any case, this kind of dicking around between Turkey and Israel will continue because politicians in both countries find it really easy to capitalize on the popularity they can gain in their own electorate by acting tough toward each other. Especially from Israel, where growing levels of fear and hysteria are going to be employed as the Palestinian statehood bid gets closer.