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Among the various statements of outrage targeted at Israel, many point to Israel's confronting the "flotilla" ships in international waters as a sign of Israel's guilt.

I direct your attention to the San Remo Manual on International Law Applicable to Armed Conflicts at Sea. Specifically, paragraph 67-68:

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67. Merchant vessels flying the flag of neutral States may not be attacked unless they:

(a) are believed on reasonable grounds to be carrying contraband or breaching a blockade, and after prior warning they intentionally and clearly refuse to stop, or intentionally and clearly resist visit, search or capture;
(b) engage in belligerent acts on behalf of the enemy;<
(c) act as auxiliaries to the enemy s armed forces;
(d) are incorporated into or assist the enemy s intelligence system;
(e) sail under convoy of enemy warships or military aircraft; or
(f) otherwise make an effective contribution to the enemy s military action, e.g., by carrying military materials, and it is not feasible for the attacking forces to first place passengers and crew in a place of safety. Unless circumstances do not permit, they are to be given a warning, so that they can re-route, off-load, or take other precautions.

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So these were ostensibly merchant vessels who were flying the flags of neutral states (since Turkey and Greece have not declared that they officially side with Hamas in their war for Israel's destruction). However, there was definitely reasonable grounds to believe that they were carrying contraband and breaching a blockade (since that was there very public, stated intention). After receiving prior warning
(see this YouTube video)
they intentionally refused to stop (I heard that they just radioed back curses in Arabic and English), and they quite clearly resisted visit, search or capture.

So this would have legitimized an attack by Israel on the vessels themselves, pursuant to paragraphs 38-46 of the treaty - note: Israel did not attack the vessels, they merely sought to prevent them from breaching the naval blockade of Gaza and redirect them to the Port of Ashdod where their supposed humanitarian supplies would then be rerouted to Gaza, along with the rest of the aid that goes in every day to not-so-starved Gaza.

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1. A maritime blockade is in effect off the coast of Gaza. Such blockade has been imposed, as Israel is currently in a state of armed conflict with the Hamas regime that controls Gaza, which has repeatedly bombed civilian targets in Israel with weapons that have been  smuggled into Gaza via the sea.

2. Maritime blockades are a legitimate and recognized measure under international law that may be implemented as part of an armed conflict at sea.

3. A  blockade may be imposed at sea, including in international waters, so long as it does not bar access to the ports and coasts of neutral states.  

4. The naval manuals of several western countries, including the US and England recognize the maritime blockade as an effective naval measure and set forth the various criteria that make a blockade valid, including the requirement of give due notice of the existence of the blockade.

5. In this vein, it should be noted that Israel publicized the existence of the blockade and the precise coordinates of such by means of the accepted international professional maritime channels. Israel also provided appropriate notification to the affected governments and to the organizers of the Gaza protest flotilla.  Moreover, in real time, the ships participating in the protest flotilla were warned repeatedly that a maritime blockade is in effect.

6. Here, it should be noted that under customary law, knowledge of the blockade may be presumed once a blockade has been declared and appropriate notification has been granted, as above.  

7. Under international maritime law, when a maritime blockade is in effect, no boats can enter the blockaded area.  That includes both civilian and enemy vessels.

8. A state may take action to enforce a blockade. Any vessel that violates or attempts to violate a maritime blockade may be captured or even attacked under international law. The US Commander's Handbook on the Law of Naval Operations sets forth that a vessel is considered to be in attempt to breach a blockade from the time the vessel leaves its port with the intention of evading the blockade.  

9. Here we should note that the protesters indicated their clear intention to violate the blockade by means of written and oral statements. Moreover, the route of these vessels indicated their clear intention to violate the blockade in violation of international law.

10. Given the protesters explicit intention to violate the naval blockade, Israel exercised its right under international law to enforce the blockade. It should be noted that prior to undertaking enforcement measures, explicit warnings were  relayed directly to the captains of the vessels, expressing Israel's intent to exercise its right to enforce the blockade.

11. Israel had attempted to take control of the vessels participating in the flotilla by peaceful means and in an orderly fashion in order to enforce the blockade. Given the large number of vessels participating in the flotilla, an operational decision was made to undertake measures to enforce the blockade a certain distance from the area of the blockade.

12. Israeli personnel attempting to enforce the blockade were met with violence by the protesters and acted in self defense to fend off such attacks.

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when the security of Israeli civilians is at stake, the government is prepared to cross certain borders, just like any goverment should.

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Well do you justify the blockade? The ships was just sending supplies to Gaza.

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The crisis is the latest in a series of Israeli decisions devised to secure the nation, and while each was to some degree tactically successful, each also further undermined its international legitimacy and increased its international isolation, policy experts here said. Those actions included building a barrier along the border with the West Bank to keep out suicide bombers; bombing Lebanon to try to disarm Hezbollah; invading Gaza in response to Hamas rocket fire; and blockading Gaza to keep out weapons.

Yaacov Bar-Siman-Tov, a professor of international studies at Hebrew University, said the nation’s leadership had failed to improve its problem with legitimacy because it focuses on tactics, like destroying enemies, rather than on a long-term strategy aimed at an ultimate settlement with the Palestinians.

“What would we like to achieve here?” Mr. Bar-Siman-Tov said. “If you would like to keep the Jewish state we have to be separated from the Palestinians. There is no way to continue with the occupation. It has created damage to our credibility and legitimacy.”

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Israel has reached the end of what they can afford to do.

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They are quickly losing any backing and sympathy they once had.

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