I didn't even read the link, but judging from all of your reactions, I gather that Israel warned the ship, and there were standard humanitarian channels that were not being used by said ship. That's the bottom line to me, if it is in fact true.
If there's a huge blackbelt dude on a sidewalk in a fighting stance telling me that I can only pass if shimmy sideways while whistling "Sweet Georgia Brown", I won't be happy about it, but guess what, I'm gonna get to shimmying and whistling! I'm definitely not going to try to walk right through him. If I want him removed I'll look for some sort of diplomatic approach, or perhaps get a bigger, badder blackbelt to remove him (which may be the underlying goal in this incident). I know my lack of fighting skills aren't going to get me anything but my ass handed to me and pity from onlookers.
Another annoying hypothetical situation:
Can you imagine what would have happened on 9/11 if authorities managed to uncover the plot after the planes lifted off but before any hit their targets, and fighter jets had managed to shoot them down? Assuming this would have been possible to do over an area that would cause little collateral damage, such a reaction would be justified in my opinion, but would be condemned the world over. There would be no way to prove that the terrorists would have actually hit the towers if left alone, and the media would turn the entire thing into innocent people being slaughtered by the U.S. military. We would be sitting here talking about how barbaric the U.S. military was, killing all of those innocent passengers without proof that thousands more would die if no action was taken.
I'm not saying that there WERE terrorists on the aid ship, and we may never know the true intentions of those on board. Perhaps they were innocent. Put yourself in Israel's shoes. What if you let them go through, then days later you find out they weren't so innocent, and they unleash havoc and bloodshed in your backyard? It's not like they went out on a Mediterranean cruise strafing random ships without warning.