Following their complaints  about the depiction or priests damaging sculptures on the Parthenon in a video on show at the New Acropolis Museum , the Greek Orthodox church has been successful in getting these scenes removed from the film.
The original video can still be seen here .
New York Times 
Scene Cut From Athens Museum Film After Protests
By THE ASSOCIATED PRESS
Published: July 25, 2009
Filed at 5:48 p.m. ET
ATHENS, Greece (AP) — A scene from an animated film shown to visitors at the new Acropolis Museum that depicts Christian priests destroying parts of the Parthenon has been deleted following protests by the Greek Orthodox Church.
The creator of the segment, Greek-born French filmmaker Constantin Costa-Gavras, has demanded that his name be taken off the film credits in protest.
”The priests used to destroy ancient temples. Now they want to remove scenes from a film,” Costa-Gavras told Greece’s Mega TV channel. ”This is the kind (of censorship) that used to happen in the former Soviet Union.”
Costa-Gavras, known mainly for French-language films with political themes, such as ”Z” and ”State of Siege”, shared an Academy Award in 1983 for best screenplay adaptation for the English-language film ”Missing,” starring Jack Lemmon, a film Costa-Gavras also directed.
Costa-Gavras’ 1-minute, 40-second segment depicting the damage done to Parthenon over the centuries — from marauding Germanic warriors in 267 A.D. to the removal of a large part of the frieze by British diplomat Lord Elgin in early 19th century — was part of a larger piece produced for the 2004 Athens Olympics and had been incorporated into a 13-minute film shown to museum visitors, narrating the history of the Parthenon from its inception to the present day.
The animated segment showed figures clad in black climbing up ladders and destroying part of the Parthenon frieze; the scene referred to well-documented episodes of destruction that took place in the early Byzantine period (5th-8th centuries A.D.), when Christians often demolished monuments and temples belonging to the old pagan era. Many parts from those temples were used to build churches. The Parthenon itself suffered some damage but was spared a worse fate by being converted into a church.
Church officials contended the film misrepresented the attitude of the Greek Orthodox Church toward Greece’s ancient heritage.
Greek media reported the segment was excised after the intervention of Culture Minister Antonis Samaras.
A Church of Greece spokesman denied there was any ”formal or informal” protest lodged with the Culture ministry but said that the church’s Holy Synod took up the matter at its latest meeting on July 21.
”The issue was discussed at the meeting, but no protest was made, either in writing or orally,” said press officer Haris Konidaris.
The Holy Synod’s press release mentions that the church will ”finance the research and writing of a study on the Church’s contribution to preserving the Ancient Greek heritage (monuments, texts).”
Museum director Dimitris Pantermalis acknowledged the Greek Church’s displeasure and, while he tried to minimize the importance of the episode, appeared irritated at those who objected.
”The segment that was cut was no more than 12 seconds long and the accompanying narration has been left intact,” he told the Associated Press. ”The film depicted a historical fact — that some early Christians destroyed, or tried to destroy, ancient monuments, and this fact remains. … I cannot understand those who said that (in) showing figures clad in black robes, we depicted priests. That’s what people were wearing in the Byzantine period, not trousers,” he said.
Pantermalis later released a statement defending the cuts in the film as ”an effort to eliminate misunderstanding and not censorship at all.”
The Acropolis Museum, which opened on June 20, now receives an average of 11,000 visitors daily, Pantermalis said.
GR Reporter 
Ministry of Culture decides to cut disputable scenes at Acropolis Museum
26 July 2009
The Greek Ministry of Culture has decided to cut the “outrageous” scenes of the 13-minute documentary, created by the world-famous Greek director Kostas Gavras, picturing the damages that the Acropolis has suffered during its 25- centurial history. As GRReporter already informed you, the Greek Orthodox Church has protested fiercely against a scene of just couple of seconds, which uses computer animation to depict angry priests in robes, destroying the Parthenon’s ornaments in the VIII century A.D. The Holy Synod has urged the Minister of Culture – Antonis Samaras – to cut the above mentioned scenes from the film. The conservative Minister from the New Democracy party has yielded to the church’s arguments and has ordered for the film to be cut.
Following the decision of the Ministry, the famous director commented: “It is sad and shameful for Greek politicians and EU members of the XXI century, to give way to the will of the Church and censure a film, which is purely based on historically proven facts.” Kostas Gavras explained that the film tried to show how during the ages, the Parthenon has suffered most from the hand of man, and if it wasn’t for men, maybe it would have remained the same as it was in the times of Pericles. “It is indeed a fact of history that the early Christian priests were shocked by the nudity of the Phidias sculptures adorning the Parthenon, and destroyed them intentionally.” The artist concludes that “With its latest reaction, the Church proves the argument that it has barely changed since the dark Medieval times.”
The 13 minute documentary is part of the educational program of the Acropolis Museum, and has already been showed in front of a big audience in the Metropolitan Opera in New York in 2004, as a part of the cultural Olympics, organized together with the Athens 2004 summer Olympic Games. People interested in the uncensored version of the film could see it at the zougla.gr website or at the following link:
Acropolis museum cuts film after Church’s protest
Sun Jul 26, 2009 5:39pm BST
ATHENS (Reuters) – Greece’s new Acropolis museum will drop some scenes of a short film by director Costa Gavras after protests from the country’s powerful Orthodox Church, the museum’s director said Sunday.
The row over the film, which informs visitors about the history of the 5th century BC Parthenon temple and depicts early Christians ruining the monument, erupted just weeks after the opening of the new Acropolis museum in June.
The Greek-born filmmaker, famous for movies such as the Oscar-winning “Z” and “Missing,” contributed a 1 minute and 40 second animation film showing figures in robes hacking at the temple to the museum’s 13 minute video presentation.
“We don’t want to offend anyone,” the museum’s director Dimitris Pantermalis told Reuters. “We will exclude this piece from the material he (Gavras) gave us,” he said, noting that a 12 second scene would be edited out of the film.
Greek media said the Church had protested to the museum. There was no official statement by the Holy Synod.
“What the clergy did back then, smashing the marbles, they are doing today (to this film),” Gavras said on the private MEGA TV channel. “If they want to show it this way … my name can’t be on the film.”
The Acropolis museum, inaugurated after years of legal battles and missed deadlines, was built partly with the aim of housing the marble sculptures removed from the Parthenon by Britain’s Lord Elgin in 1806. The so-called Elgin marbles are exhibited at the British Museum in London.
Greece’s Orthodox Church officially represents more than 90 percent of the 11 million strong population. Early Christians tore down statues and temples in a effort to eradicate paganism.
(Reporting by Renee Maltezou, editing by Elizabeth Fullerton)