How would that make a difference? The blockade starts at the border of international waters and once the boats reach that line, they're breaching the blockade.
For what it's worth, I'm no blind defender of Israel, especially with the current government and Prime Minister. I object to the building of new settlements and I'm really not a fan of the blockade. In fact, my first reaction on hearing about the Mavi Marmara was "What the fuck?! Why would they do something so stupid?", but having read all about all actually that happened on the boat, I can't help but admire the navy's restraint in these matters.
Here is an article that explains the events as they unfolded. A quick precis: When the Mavi Marmara was approaching the blockade, the navy requested that they instead go to Ashdod Port and from there the government would provide trucks to transport the supplies to Gaza under the protester's supervision. As you can see in the following video, they refused; they cared more about making a statement than any humanitarian act.
The commandoes planned to land on the boat, go to the bridge and redirect the boat to Ashdod. Unfortunately, they misjudged the nature of the people on board; thinking that they were just peaceful protesters, they came down holding paintball guns (it seems silly, yes, but they're less dangerous in close range than rubber bullets). Their handguns were holstered and they were only given the order to open fire after all the commandos were attacked and the first one was pushed off the main deck to one much lower down. Even still, the orders were to attempt non-lethal force and just shoot at their legs. Check out the following video to see what it was like (and be warned, the violence is quite sickening)
And if anyone still believes that the people on these boats had peaceful intentions, this last video will change your mind.
Anyway, go and read this article that I mentioned previously. It describes the whole thing much better than I can.