Mayor Shirley Franklin urged the congregation not to pay tribute to King's message of peace and justice on his birthday and then contradict it the next.
"Millions can't find jobs, have no health insurance, and struggle to make ends meet, working minimum-wage jobs. What's going on?" Franklin said, repeating a refrain from soul singer Marvin Gaye.
As King condemned the war in Vietnam 40 years ago, Ebenezer's senior pastor, the Rev. Raphael G. Warnock, denounced the war in Iraq.
"The real danger is not that America may lose the war," Warnock said. "The real danger is that America may well lose its soul."
Visitors also paid homage to the slain civil rights leader and his wife at their tomb, not far from the church.
"They're together at last," said Daphne Johnson, who was baptized by King at Ebenezer.
Coretta Scott King died last year on Jan. 31 at age 78. An activist in her own right, she also fought to shape and preserve her husband's legacy after his death, and founded what would become the Martin Luther King Jr. Center for Nonviolent Social Change.
Crowds lined up early at the Atlanta History Center to see the first exhibition of King's collected papers since they were returned to his hometown. The papers brought back difficult memories for some.
"I remember a lot that I don't care to say," said Bertis Post, 70, of Atlanta, who marched with King in Alabama and Atlanta. "I always wanted to see the papers in person -- just to be here and be around what you believe."
The exhibit includes King's letter from the Birmingham jail, an early draft of his famous "I Have a Dream" speech, his acceptance speech for the Nobel Prize, and more than 600 other personal documents.
Elsewhere, thousands of volunteers observed the holiday by taking part in service projects. Organizers expected about 50,000 people to participate in about 600 projects, said Todd Bernstein of the MLK Day of Service.
President Bush, in an unannounced stop at a high school near the White House, said people should honor King on the holiday by finding ways to give back to their communities.
Classes were not in session, but volunteers were sprucing up the school.
