It appears that it was the BC government that authorized the killing of the eagles. Andrew Bryant, head of the Marmot Foundation, has co-authored many papers with the government's Doug Janz, who is mentioned in the article below, so it is surprising that the Foundation appears not to have been consulted before this cull was undertaken.

Blaming eagles, cougars and wolves for killing marmots is an easy path to take. The decline of the marmot correlates with the logging that flattened the land, thus giving easy access to predators. All the toxic chemicals used in the Nanaimo estuary, right in Nanaimo's watershed, have probably done more damage to the marmot population than all the predators put together. It will also make it difficult for them to be re-established in this area.

Marmot recovery plan under fire

By JANE ARMSTRONG
Thursday, March 18, 2004
From Thursday's Globe and Mail

Vancouver — In a West Coast environmental saga replete with a Solomon-inspired subtext, the much-loved and endangered Vancouver Island marmot has been pitted against the majestic — though not quite so rare — golden eagle.
The B.C. government authorized the killing of six eagles because they were a threat to the marmots, whose numbers have dwindled to less than two dozen in the wild. The killings were authorized by the Ministry of Water, Land and Air Protection but never made public, a move that has riled B.C.'s scientific and conservation community.
They're angry the government took it upon itself to kill one species to save another. Conservationists also predicted the move could backfire because it doesn't address the broader reasons for the marmot's decline, such as logging.
"Morally, I think it's absolutely indefensible," said Victoria ecologist Chris Darimont, who had heard rumours of the eagle kill for months. "It's outrageous." The eagles were shot because they — like cougars and wolves — prey on marmots.
The eagles, protected under Canadian law and international treaties, were lured to their deaths with a deer carcass placed at the foot of a mountain near Nanaimo, about 100 kilometres north of Victoria. They were shot when they landed on the dead deer to feed. The province has the authority to kill eagles as a predator-control measure.
Members of the charitable organization set up to save the marmots were not told of the plan to kill the eagles. As late as last month, the foundation was sending out letters to donors saying the eagle rumour was false.
"I was disappointed," said Rick Page, scientific adviser to the Marmot Recovery Foundation. "The government took this action on its own. There appears to have been a miscommunication. They did not tell us."
He said he learned of the killings two weeks ago after a reporter made inquiries. He contacted Doug Janz, who heads the ministry's fish and wildlife section, who confirmed that six eagles were killed over two winters ending in 2003.
The incident has reignited the debate over the methods used to save the marmot. Only 21 are left in the wild and an ambitious recovery plan has not achieved hoped-for results.
That plan, which includes breeding marmots in captivity in zoos in Calgary and Toronto with the goal of reintroducing them to their mountainous Vancouver Island habitat, has had disappointing results.
Last summer, three of four captive-bred marmots let loose were eaten by predators within weeks, as were another three wild marmots.
To control predators, the ministry has in the past encouraged hunting of wolves and cougars in the marmot habitat near Nanaimo, a move that has drawn criticism as well.
However, cougar and wolf hunts have existed for years on the island.
The marmot recovery team plans to release more captive-bred marmots to Vancouver Island mountaintops this summer.
It hopes for better results, but will urge the government to stop killing predators. Instead, it has suggested a plan to use shepherds to guard the marmots.
It was a University of Victoria biology teacher who learned of the dead eagles.
Neville Winchester made the discovery after receiving a call from a ministry staffer in Nanaimo, asking him to collect a dead eagle.
Mr. Winchester, who uses animal carcasses to teach, assumed the eagle had died of natural causes. When he opened the freezer in Nanaimo, he counted at least six eagles. "I said: 'Wow. Where did you get them?'."
The ministry staffer said that the birds had been killed to protect the marmots.
Golden eagles are found throughout North America. The birds of prey are distinguished by a golden wash on the back of their heads and neck.
The ministry has defended the eagle kill. In an interview, Mr. Janz said eagles had long been identified as a main threat to marmots.
Four eagles were killed in 2002, he said, and two more in 2003. It was a tough decision, he said, but the marmot recovery plan has reached a pivotal juncture: If the captive-bred marmots can't survive on their own in the wild, the species will be doomed — and soon.
He also noted that none of the predators killed are endangered — including the eagles
In hindsight, Mr. Janz, said it might have been wise to inform the public and marmot foundation of the eagle kill, but insisted the cull wasn't secret.
He noted that predator control is part of the ministry's mandate. However, no more eagle kills are planned, he added.