The heavy-handed removal of Walter Wolfgang on Wednesday backfired for the Labour leadership, with some delegates saying it reflected an internal climate which put too much emphasis on maintaining control and silencing dissent.
"You cannot stifle debate by hiring heavies," said Wolfgang, who received a hero's welcome as he returned to the conference.
"We made a mistake, I believe, in invading Iraq without cause. We've got to rectify it by withdrawing from Iraq. If you try to ignore it, it will not go away," he said.
Wolfgang's expulsion was splashed across the front pages of several national newspapers and dominated the news on the final day of the meeting in the seaside town of Brighton.
"This indicates a wider culture of control and intolerance of dissent," said David Clark, a former adviser to the late Robin Cook, one of Labour's most prominent opponents of the war.
But Defence Secretary John Reid, who also apologised to Wolfgang, insisted Labour had a culture of being able to debate controversial subjects such as Iraq without questioning other people's integrity or sincerity.
Anger over the decision to back the 2003 US led invasion split Labour and Britain and continues to dog Blair.
"People are perfectly entitled to freedom of speech in our
country ... and I'm really sorry about what happened to Walter and I've apologised to him"
British Prime Minister
Analysts say the prime minister's fate is inextricably linked to events in Iraq, where British troops came under heavy attack this month and elections are set for December.
Blair won a third straight term in May but opposition to the war contributed to a slide in Labour's parliamentary majority.
The prime minister has said he will not run in an expected 2009 election but he seems keen to stay for several years before he is expected to hand over to finance minister Gordon Brown.
Burly stewards grabbed Wolfgang and bundled him out of the conference on Wednesday after he interrupted Foreign Secretary Jack Straw as he said British troops were in Iraq to help build a secure and stable country and would stay as long as needed.
"That's a lie and you know it ... Rubbish," shouted Wolfgang, a refugee from Nazi Germany and a party member for 57 years.
Wolfgang was briefly arrested using anti-terrorism powers. "People are perfectly entitled to freedom of speech in our
country ... and I'm really sorry about what happened to Walter and I've apologised to him," Blair told BBC Television.