Uniformed officers wearing facemasks and a group of people dressed in blue overalls and goggles arrived at the farm in Wickwar on Tuesday morning.
Ms Macdonald, who launched a four year legal battle in an attempt to save her pet, said: “All the time they were simply planning to murder Geronimo.
“This is yet another appalling demonstration of bad faith and duplicity by the Secretary of State and everyone at Defra.”
Chief Veterinary Officer Christine Middlemiss said: “This is a terribly sad situation and our sympathies remain with all those affected by this devastating disease.
“No one wants to have to cull infected animals if it can be avoided, but we need to follow the scientific evidence and cull animals that have tested positive for bTB to minimise spread of this insidious disease and ultimately eradicate the biggest threat to animal health in this country.”
The destruction warrant issued by the court was valid until September 4.
Downing Street has expressed sympathy for Helen Macdonald, with the Prime Minister's official spokesman saying: "It's obviously highly distressing for someone to lose animals to TB and that's a situation that farmers sadly have to face.
"Our sympathies are with Ms Macdonald and any others that are affected by this terrible disease."
Ms Macdonald wanted the Government to allow Geronimo to be tested for a third time or let him live to aid research into the disease.
A camera broadcasting a livestream of Geronimo’s pen was set up so supporters could watch for Department of Environment, Food and Rural Affairs (Defra) officials arriving.
Footage showed Geronimo attempting to escape by running into a field with other alpacas. But several officials followed the animal, tied a rope around it and led it away.
Supporters, who have been camping out at the farm, attempted to try and stop the animal being removed.
Ms Macdonald said: “Geronimo has been manhandled out of my farm.”
When asked how force was used, she added: “You'll have to ask the poor witnesses that witnessed him being rounded up and dragged into a horsebox. These are barbaric actions of unscientific, abusive people in Government.”
A Defra spokesman said a post mortem examination would now be carried out by veterinary pathologists.
It will include a “bacteriological culture” of tissue samples, which can take up to three months.