By early Thursday, planes carrying hundreds of activists, along with the bodies of the nine killed in the raid, flew to Turkey and Greece, as others were released through Jordan. Hundreds of relatives and well-wishers cheered outside the airport as they landed in Istanbul, Turkish television showed, while the deputy prime minister stood atop a bus, declaring that “diplomacy had resulted in success for now” but that “these murders” would be pursued “within the scope of law.”

The release seemed most immediately aimed at repairing dangerously eroding ties with Turkey, Israel’s main ally in the Muslim world, as demands continued to intensify around the world to end a blockade that critics say has kept Gazans isolated and impoverished.

And in fact the homecoming seemed to deflate some anger in Turkey, which had made the release of hundreds of its citizens its main demand after at least four Turks were killed by Israeli commandos in the raid. The Turkish foreign minister, Ahmet Davutoglu, who had spoken earlier with Secretary of State Hillary Rodham Clinton, sought to ratchet down tensions, saying, “It was time that calm replaces anger.”

Still, Turkey, which withdrew its ambassador to Israel, continued to press for an end to the blockade as a condition for restoring full diplomatic relations.

Even as Israel sought to improve its international standing with the quick prisoner release, it again defended the raid. Prime Minister Benjamin Netanyahu, in a television address on Wednesday night, said the blockade was necessary to prevent rockets and missiles from being smuggled to Hamas, which governs Gaza, and other anti-Israel militants.

“Opening a naval route to Gaza will present enormous danger to the security of our citizens,” he said. ‘Therefore, we will stand firm on our policy of a naval blockade and of inspecting incoming ships.”

Israeli officials quickly responded to a legal challenge by reserve officers asking the Supreme Court to hold the prisoners for prosecution. With hundreds of detained activists waiting in Ben-Gurion International Airport to board planes sent by Turkey and Greece to take them home, Israel’s attorney general, Yehuda Weinstein, wrote to the court saying that the decision was based on “clear diplomatic interests touching on the state of Israel’s foreign relations and national security.”

Some news reports said that as few as three activists remained in detention. But despite the somewhat softer words on Wednesday, there was no telling if the gesture would be enough to roll back longer-term damage to Israel’s relationships, especially with Turkey, which has grown increasingly angry at Israel. The Turkish Parliament issued a resolution calling on the government of Prime Minister Recep Tayyip Erdogan to “reconsider all political, military and economic relations with Israel,” and newspaper headlines blared discontent. “Nothing will be the same,” declared Hurriyet, a Turkish daily.

The uproar was ignited when Israel sent its commandos into international waters to stop the flotilla carrying humanitarian aid, including construction materials, toys and used clothes, to Gaza. Commandos boarded five ships without incident, but when they dropped from helicopters onto the largest, the Turkish-owned Mavi Marmara, soldiers opened fire when they said they were attacked by passengers with chains, knives, bars and clubs. Nine people were killed.

It appears unlikely the conflict will fade soon. With at least one new ship already setting sail to challenge the sea blockade, another flotilla being planned in London, the United Nations Human Rights Council in Geneva voting to create a committee of investigation and Secretary General Ban Ki-moon saying Israel’s policy “punishes innocent civilians,” Israeli officials maintained they would not relent.

The defense minister, Ehud Barak, praised the commandos on Wednesday. “We need to always remember that we aren’t North America or Western Europe; we live in the Middle East, in a place where there is no mercy for the weak and there aren’t second chances for those who don’t defend themselves,” he said.

The dual images of Turkey as a guardian of Palestinian rights, and Israeli soldiers shooting unarmed civilians, undermined the credibility of Arab capitals allied with the West, regional foreign policy experts said. Egypt, Jordan and Saudi Arabia, which have pressed for a comprehensive peace with Israel, were placed on the defensive as Turkey, allied with Iran, Syria and Qatar, has gained credibility through its support of Hamas.

Egypt felt so exposed by the events at sea that it opened the border between Gaza and Rafah. Egypt has withstood criticism for keeping its border mostly closed, even during the 2008 Israeli invasion in Gaza. Egypt has argued that opening the border would undermine its own security and leave it as the de-facto administrator of Gaza. Egypt also does not want a Hamas-ruled enclave on its border, fearful it will spread the group’s militant Islamic ideology over the border. Still on Wednesday the border was opened. More than 600 people crossed Gaza into Egypt.

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.”

There is some indication that some rethinking of the leadership’s approach has begun, said Ron Pundak, director of the Peres Center for Peace. He said that more Israelis recently attended a demonstration outside the Ministry of Defense than they had at the start of the Gaza invasion. “Maybe we are waking up,” he said.

Reporting was contributed by Neil MacFarquhar from the United Nations, Sabrina Tavernise and Sebnem Arsu from Istanbul, and Mona El-Naggar from Rafah.