The IDF attacked the flotilla in international waters, [and there was no preliminary attempt to turn the boats back by other means -- commando raid was the tactic of first choice][Incorrect: see update]. When the soldiers boarded, they were met with stiff resistance -- the first ones were clubbed and and least one was thrown overboard. In response to this resistance, the IDF soldiers opened fire, and 10-19 activists from the flotilla were killed. No IDF commandos were killed.
The IDF maintains a blog, where you can see their portrayal of the event. It prominently features video of the raid, showing the first commandos aboard being beaten, and photos and video showing the assortment of kitchen knives, metal pipes, and sundry other weapons deployed by the activists in their attempt to ward off the raid. The blog refers to the activists' resistance this way: "the activists on board lynched the soldiers in a planned attack."
So, an army raids vessels flying the flag of an allied state, in international waters, [with no warning,][Incorrect. See update.] and those raided are supposed to meekly surrender. If they don't, then they are guilty of a planned attack on the soldiers raiding their boats.
There is a logic to this, but it is not the logic of the law, or the legal state. It is, in the Foucauldian idiom of neo-Marxism, the logic of the norm. Israel has a policy of containment regarding Gaza. The flotilla represented a risk to that policy. It broke no laws and posed no military threat, but, as a risk, it was the object of military intervention. As an identified risk, the burden was on the activists to prove, not their innocence, but their passivity. Since they actively resisted, they had to be pacified, and retroactively proved themselves to be the risk they had been identified as. The citizenship of the activists is of no import; they could have been Israeli, or Iranian, or American, or whatever -- there is no citizenship per se in relation to states acting as imperial agencies. The only question is whether you are passive with regard to empire or pose a risk.
This same logic pervades the quasi-militarized police operations that we call the war on drugs and the war on terror. What happened in the Mediterranean is of the same form as what happens in drug raids in Indiana, or in mobilizations against protesters in Minneapolis. As Foucault says near the end of his lectures on "The Birth of Biopolitics," the "law and order" mantra of conservatives has been revealed to be a contradiction in terms -- the question is: Law or order? The postmodern state -- empire -- chooses order.
I don't know where I got the "no warning" tidbit, but that's not right. The IDF announced they were boarding to search the ships. For discussions of the legality of Israel's blockade and of this raid, see here, here, and here.
Well, maybe the "no warning" tidbit was right after all. As accounts from activists have started seeping out, the raid looks worse and worse -- see here and here, for example.
Also, regarding the new status accorded "citizens" of the postmodern state, see here.