Jim Seida / NBC News

Syrians gather in London's Trafalgar Square on Thursday to protest the Assad regime.

LONDON -- As the Olympic torch made its way into London's famous Trafalgar Square, Ammar Masarani stood wrapped in the flag of the Syrian uprising against the murderous regime of President Bashar Assad among a crowd of about 50 other dissidents.

They had waited for almost two hours this moment to highlight the slaughter of more than 10,000 of their countrymen. As the torch went by, they waved their flags, but remained largely silent in order, Masarani said, "to stay within the rules." 

"Most people don't know what's going on in Syria with the Assad regime, so we are out here to raise awareness," Masarani told NBCNews.com. "I'm from Homs, he [Assad] has destroyed most of my city. He's destroyed most of the cities, Homs, Daraa, Hama.  He destroyed them and now he's starting in Damascus and Aleppo."

Given the scale of the problems in Syria, Thursday night's flag-waving demonstration might be a small gesture. However, it is the kind of protest that the Olympic organizers seek to avoid, insisting firmly that sports and politics should not mix and that the high ideals of "Olympism" must not be sullied by partisan campaigns.

More coverage of the Syria conflict

But experts who spoke to NBCNews.com accused the International Olympic Committee of picking and choosing what to regard as political while spinning the "fairy tale" of neutrality, suggesting it was time for the movement to acknowledge reality.

The present IOC's badly handled refusal of the request for a minute's silence for the victims of the Munich massacre at Friday's Opening Ceremony is perhaps case in point. Since the 1972 Games, the Olympics has done little to formally commemorate the dead, and relatives and Israeli officials had hoped the 40th anniversary would provide an appropriate opportunity.

Slideshow: Athletes killed at 1972 Munich Olympics

Keystone / Getty Images

Eleven Israeli athletes and coaches were killed by Palestinian gunmen during the 1972 Olympic Games in Munich, Germany.

Launch slideshow

Instead, IOC President Jacques Rogge and several leading figures in the U.K. held a minute's silence in the Olympic Village on Monday at short notice and without publicizing what they were doing -- after what Rogge described as a "spontaneous suggestion" -- but that only seemed to add insult to injury.

Daniel Taub, Israel’s ambassador to the U.K., told NBCNews.com that the Munich massacre was "beyond politics." The Embassy was holding its own minute's silence Friday, after a last-ditch plea to Rogge by the widows of two of the hostages fell on deaf ears.

"We’re talking about the darkest moment of Olympic history," Taub said.

Toby Melville / Reuters

Sebastian Coe (left), chairman of the London Olympic organising committee, and other officials mark a minute's silence at a ceremony in the Olympic Park in East London on Monday. President of the International Olympic Commission, Jacques Rogge paid tribute to the 11 Israeli team members who were killed at the 1972 Munich Games at a ceremony at the Athletes Village in London on Monday.

“An attack on the Olympic ideals of peace and harmony through friendship and solidarity really requires remembering publicly within the Olympic framework. I would say that’s not politics, it’s humanity. The fear is that a failure to do that becomes political," he said.

“I would say in a very real way the people calling for a remembrance are really standing up for the true ideals of the Olympic Games, not trying to betray them," he added.

Taub said Israelis were puzzled that “something that seems to be such a clear violation of Olympic ideals doesn’t seem to be deserving of commemoration.”

Ilana Romano, widow of Yossef Romano, an Olympic boxer killed in 1972, returned to Israel Thursday from England where she made a personal plea to the IOC to relent. She told NBCNews.com that she hoped spectators would stay silent and the media would turn off their microphones for a minute while Rogge speaks at the Opening Ceremony.

'Pandora's Box'
Jules Boykoff, a former U.S. soccer player and an associate professor in Pacific University’s department of politics and government, said the IOC should recognize they are involved in politics and consider setting up a committee or some other formal way of dealing with such issues.

Boykoff, who is in London researching a book about the Games, said this would open "a kind of Pandora’s Box in terms of the issues they might have to deal with,” but scorned the claim that the Olympics is apolitical.

“The idea that sports and politics don’t mix is a fairy tale that the IOC tells itself to help it sleep better," he said. “It’s obviously thrumming with politics at every level.”

He said an Olympic political commitee might get decisions wrong, but at least people would know “here’s where we [the IOC] are coming from."

More London 2012 coverage from NBCNews.com

There are suggestions that at least some political issues are decided in secret, for example when planning where to put different nations -- perhaps arch-rivals such as Israel and Iran -- in the Olympic Village. (On Monday, Iran announced that its athletes would compete against Israelis in London. The country faced criticism after some competitors withdrew from events against Israelis at the 2004 Athens Games and 2008 Beijing Games.)

"Politics is taken into account when choosing who goes where, but that's based on guidance at International Olympic Committee level, not by [organizers of] London 2012, and it's agreed by each country in advance -- they know who their neighbors are going to be," a senior official involved in operations told NBCNews.com.

"It's about making sure athletes are comfortable in their living space rather than which countries don't get on," the source said. "Even then, it's a not really an issue. You've got to remember that these guys compete alongside each other all the time and all over the world --they know each other, some of them are best man at the other's wedding and so on." 

However, London 2012 organizers LOCOG denied international diplomacy played any role in the allocation of areas in the athletes' village, saying in an emailed statement "political issues are not a factor."

The Olympic movement does sometimes make open forays outside the world of sport. The Olympic truce, for example, calls for fighting around the world to stop for the duration of the Games.

But, in case anyone was thinking this might offer hope for countries like Syria, Boykoff was scathing. This "really nice idea" was "sort of a farce," he said. "Battles are going to continue across the world, they are not going to stop for the games, as popular as it is."

Flag flaps
Apart from the flag of the Syrian opposition, other flags have been already been causing political controversy at London 2012.

The Games actually began Wednesday with several soccer matches, one involving the North Korean and Colombian women's teams.

North Korea came out to train in Glasgow's Hampden Park stadium, but then walked off the field and refused to return after the South Korean flag was mistakenly used by officials. The game eventually did take place about an hour later with the North Koreans winning 2-0.

On Friday, it emerged that Taiwan's flag had been removed from among a host of others on London's Regent Street over concerns that China would be offended. Taiwan, which China views as a breakaway province, uses the flag of the Chinese Taipei Olympic Committee at the Games, after the IOC ruled it could not use its own flag in the early 1980s.

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And a marathon runner from new nation South Sudan, Guor Marial, will compete under the Olympic flag, after he understandably turned down the chance to run for Sudan -- which fought a decades-long civil war with the South that ended in the latter's independence. He was unable to run for his own country because it has not yet become a member of the Olympic movement.

But apart from Marial, everyone else will be competing for their country and Alan Bairner, professor of sport and social theory at the U.K.'s Loughborough University and author of a book, "The Politics of the Olympics," said the Opening Ceremony would be "replete with the politics of nationalism."

This runs contrary to the initial desire of the founder of the modern Olympics, Pierre de Coubertin, for athletes to compete as individuals rather than in state teams to avoid overly nationalistic sentiment.

“They talk about the world coming together, but the world comes together with national flags and anthems," Bairner said. "Events at Hampden Park … clearly demonstrated the significance of flags and emblems at supposedly apolitical events –  particularly if the organizers don’t get it right."

Bairner said only flags of competing nations were allowed to be flown at Olympic events and questioned what would happen if the flag of Scotland – part of the United Kingdom – was flown or given to a successful Scottish athlete as they celebrate.

 Scotland has also been racked with concern over the entry of a Team Great Britain in the soccer event. Despite being one country, the U.K. has four international soccer teams -- England, Scotland, Wales and Northern Ireland -- and other countries have questioned whether this is fair. The fear in Scotland particularly was that a Team GB would set a precedent that would lead to the demise of the Scottish national team.

Bairner, a Scot, said the idea was almost unthinkable. "I can't imagine life without Scottish teams in these competitions [the World Cup, European Championships etc]," he said. "For it just to become Team GB, I would lose interest and support Spain or Germany."

He suggested the loss of the Scottish soccer team would provide a "boost" for supporters of independence from the U.K. ahead of a referendum on the issue in 2014.

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Bairner said the IOC tended to pick and choose what they deemed to be political.

It was possible, he said, that the IOC thought a Munich commemoration at the Opening Ceremony would be viewed as “pro-Israel.”

But he suggested it was “just about remembering people who died at an Olympic Games,” and said he thought most people would be "comfortable" with the idea.

Bairner, who said his sympathies tended to be with the Palestinians, said it was difficult to see how anyone could “object too strongly because they would almost be condoning that kind of activity,” and suggest that Olympic athletes were “legitimate targets.”

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The ad hoc approach to political issues has been going on for years.

A few months before the Beijing Games of 2008, Rogge declared firmly that it was a "sporting, not a political, association," as he dismissed the effect of the resignation of filmmaker Steven Spielberg as artistic consultant over China's support for Sudan amid the Darfur conflict.

And in 1936, Avery Brundage, then head of the American Olympic movement and later an IOC president, opposed a boycott of that year's Berlin Games in Nazi Germany for the same reason.

The IOC’s decision to go ahead with the 1936 Munich Games -- awarded before the Nazis came to power partly to help shore up Germany's ailing democracy -- had handed Adolf Hitler a "huge propaganda victory,” Bairner said.

“You compare that with 1968 when [athletes] Tommie Smith and John Carlos do the Black Power salute. They are punished by the IOC for bringing politics into sport," he said, in perhaps an indication of what might happen to any Syria athletes trying to draw attention to the ongoing bloodshed in their country.

AFP - Getty Images, file

U.S. athletes Tommie Smith (center) and John Carlos (right) raise their gloved fists in the Black Power salute after receiving their Olympic medals on Oct. 17, 1968.

The treatment of Smith and Carlos likely gives an indication of what might happen to any Syrian athletes who attempt to use the Games to protest the killings in their country.

“It seems they [the IOC] decide what is political at any given time … what they approve of and don't approve of. That’s when they become quite a slippery organization," Bairner said.

NBCNews.com submitted requests for comment from the IOC about the issues raised in this article on Wednesday and Thursday.

Media relations manager Sandrine Tonge said a response would be provided "as soon as we can."

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