There are more than a few people out there who are saying, “Israel should have understood that it would have been better to simply let the ships through. Some have compared the Mavi Marmara with the Exodus. They were both ships trying to run a blockade, but the DIFFERENCE between the two makes all the difference.
In the case of the Exodus, Jews who had no other place to go, were willing to fight and die for THEMSELVES to live. The British were trying to appease the Arab population by preventing more Jews from arriving. Haj Amin Al Husseini led riots and pogroms against the Jews already in the land. The British wanted to make nice with the Arabs in order to advance their political and economic interests. The Jews were stateless and scattered. They had no possibility of creating a state of their own if not in Judea, whose name was changed by Rome  to Palestina, after the historic enemies of the Jews in order to spite the Jews.
In the case of the Mavi Marmara, the activists were trying to aid those who are fighting and trying to kill the Jews. The humanitarian aid was going to get to Gaza no matter what, they already knew that. Israel would have handled it as it had in the past. The only reason to resist what they were told was going to be a non-violent takeover of the ships was to prevent that from happening. One could argue that they intended to run the blockade and hoped that their resistance would prevent the Israelis from taking the ship. One could even argue that they may have intended to capture or kill Israeli soldiers to make that happen.
Those on the Mavi Marmara were not fleeing for their lives and not fighting for their lives, at least not until they created a situation in which that was indeed the case. Even then they were not fighting for their lives because of who they were, but because of the actions they had done in those very minutes. That some innocents may have perished, people who had not used violence, is unfortunate to say the least. Tragic in fact. But that some attempting to kill were killed is tragic only in the fact that they were motivated not for peace for all, but for the peace of some, Gazans, at the expense of others, Israelis.
Israel faces mortal enemies in Gaza. Not only in Hamas, but in other even more radical groups that are not controlled by Hamas including affiliates of Al Qaida. Militants regularly fire home made rockets out of Gaza. Most fall harmlessly in fields, but occasionally they do real harm. While “aid ships” might well not have problematic cargo, especially if those sending them know that they will be seized and searched, they certainly might if they were not going to be seized or searched. This is the necessity of the blockade. So long as there is no peace between Israel and the Palestinians, the threat that long range missiles entering Gaza would have is beyond question, they would come from Gaza against Israeli civilian targets.
Israel fought a war that resulted in hundreds dead to stop small scale rockets and destroy medium range ones. How much more must it fight to stop the importation of long range missiles into Gaza??? Those who do not understand this necessity on Israel’s behalf cannot possibly contribute to peace in the Middle East. If Hamas were to gain more military strength, it would simply escalate violence and bloodshed on both sides going forward.
That is why Israel had no choice.