The so-called Gaza flotilla, comprising eight ships and roughly 800 participants, was not put together by peace-loving humanitarians primarily worried about relieving the suffering of Gaza residents. The people of Gaza already have access to food, medicine and other relief supplies provided by both Egypt and Israel. But both countries have sought to limit the importation of military equipment or dual-use materiel that can be employed for military purposes by Hamas. That terrorist organization controls the Gaza Strip and is unabashedly dedicated to Israel’s eradication. It is also closely linked with the Muslim Brotherhood, which is dedicated to the overthrow of secular dictator Hosni Mubarak and the creation of a theocratic regime in Egypt.

The flotilla was organized by the Turkish group Insani Yardim Vakfi (Humanitarian Relief Foundation), which bills itself as a philanthropic organization. But both the Danish Institute for International Studies and the Israeli Intelligence and Terrorism Information Center have documented copious links between Insani Yardim Vakfi and the global jihadist terrorist movements including al Qaeda. One of Insani Yardom Vakfi’s activists, Izza Shahin, was arrested by Israeli forces in the West Bank recently and expelled on charges of transferring tens of thousands of dollars to Hamas-controlled “charities.”

Other members of the flotilla came from such organizations as the Egyptian Muslim Brotherhood. Al Jazeera quoted one woman aboard the flotilla saying “Right now we face one of two happy endings: either Martyrdom or reaching Gaza.”

From Israel’s vantage point this was a no-win situation. Allow the ships to dock in Gaza and they would unload supplies that might be used to arm Hamas. Stop the ships and you risk a public relations disaster, which is exactly what happened.

First the ships ignored repeated warnings from the Israeli navy to turn back or to put into the Israeli port of Ashdod where the supplies could be off-loaded, inspected, and, if purely humanitarian, sent on to the Gaza Strip. They kept on sailing even after Israel publicly warned that its commandos would board the vessels.

Most of the boardings, with commandos rappelling down ropes from helicopters, went smoothly. But aboard the largest vessel, the Turkish-flagged ferry Mavi Marmara, the passengers and crew put up a violent resistance. The Israeli Defense Forces have released video showing a commando being hurled from the top deck. Other commandos were confronted by an angry crowd armed with metal poles, knives, even reportedly firearms and firebombs.

The details are still confusing, but it’s clear Israeli commandos were wounded in the melee and were in danger of being killed. They had hoped to avoid violence and were armed with paintball guns, but the boarding team felt compelled to open fire to prevent themselves from being overrun.

It is hard to second-guess the actions of men in combat who feel their lives are in danger, but that won’t prevent the whole world from trying. Turkey’s Islamist prime minister, Recep Tayyip Erdogan, described the incident as “state terrorism” and called his ambassador home from Israel. Palestinian Authority President Mahmoud Abbas called the incident “a massacre.”

Non-Arab leaders didn’t go that far but French President Nicolas Sarkozy did call the use of force “disproportionate”—the favorite epithet applied nowadays to all Israeli military actions, even those (like the assassination in Dubai of Hamas official Mahmoud al-Mabhouh) that only kill well-known terrorists.

Israeli officials are right to say the operation was justified and that the blood was on the hands of the pro-Hamas activists. Right, but irrelevant.

As it does too often, Israel took a narrow military operational approach to what is a broader strategic problem. Hamas, Hezbollah and other terrorist groups are conducting a skillful “information war” that is making Israel a pariah state in the international community. Israel, like the United States and other democratic nations, is at a severe disadvantage trying to combat a ruthless foe willing to sacrifice its own people to score propaganda points.

There are no perfect counter-tactics available, but whenever Israel does use military force it needs to be more aware of the political ramifications. That awareness appeared to be lacking during the botched 2006 war against Hezbollah—and in the boarding of the Gaza flotilla.

One wonders if it wouldn’t have been possible for Israeli agents to sabotage the ships before they left port so that this incident would never have occurred? Or failing that, to allow the ships to be off-loaded in Gaza and then disable them so as to prevent any further trips.

That is only speculation from afar. Neither I nor any other outsider can know all the factors that went into Israeli planning. But, whatever the intent, the outcome was a fiasco that Israel doesn’t need when its relations with the United States, its most important (and virtually sole) ally, are already at a low point.

Mr. Boot is a senior fellow in National Security Studies at the Council on Foreign Relations.