Pfftlol, commence israel hatred.
If you had read the article thoroughly, you would've noticed that they were attempting to break past a blockade. Isreal had repeatedly warned them not to.
And you overstate your case. The activists definitely attacked with both GUNS and knives. The soldiers may have overreacted, but they certainly had reason to fire.
To me the most controversial thing is stopping an aid flotilla to begin with. Why would they bother? Did they suspect terrorists were aboard? Did they have any evidence?
As to the Turkey problem, they do not need to "fire on the ship," they just yell gtfo, use a naval blockade, or let them pass. They will definitely not try to inflammate NATO, which is giving them ground troop support against terrorists. And of course a visit sanctioned by an official government bears a much smaller risk to Israel's security.