How do you solve a problem like Marius?

Zoos have had a pretty bad press this week. Copenhagen Zoo's killing of Marius, a healthy baby giraffe, and feeding him to lions as an educational exercise, was probably not the best way to advertise how well it was doing at breeding endangered giraffes. And now a second giraffe (also called Marius) may be culled in Denmark next week. If you are a giraffe in Denmark right now, you might be checking to see if you're called Marius.

The first Marius should have been a huge success story for the modern zoo system, where accredited members agree to follow collective guidelines and husbandry techniques to promote the breeding of selected rare species. In Europe, this is co-ordinated by Eaza, the European Association of Zoos and Aquaria. It's an enormous operation involving thousands of animals across 347 zoos, mostly in Europe. And because of extremely stringent entry requirements – mere membership of your national zoo governing body, for instance, does not automatically qualify you to join – it is safe to say that these are 347 of the best zoos in Europe.

By pooling resources and expertise, they achieve far more than individual members, or any zoo outside their membership, can achieve on its own. In terms of the human race trying to do the right thing by animals, Eaza is one of the best forums on the planet.

Thirty-eight zoos co-operate to breed reticulated giraffes, such as Marius I. Producing a surplus of such rare animals is a huge achievement. There are 240 left in the wild, plus 126 in European zoos. The captive population is rising, while those in the wild decline.

I watched Bengt Holst, scientific director at Copenhagen Zoo, defend his actions on Channel 4 News, and agreed with him right up to where he said: "And so we decided to euthanise the giraffe." Inside the breeding programme, no space was available. Outside the programme, he felt, he couldn't guarantee welfare. But if, for instance, Eaza readily sanctioned non-breeding groups in zoos with national-level accreditation, then Holst would have had more choices, and Marius would be alive today. But would he breed? And where would his offspring go?

The day after Marius died, I did the whole "should we close all zoos" TV debate with Peta, the animal rights charity. It's easy to say that animals don't belong in cages, but is now the time to shut those 38 facilities, and release all the giraffes into the declining wild population? If you put 10 animals into the wild, eight will almost certainly die from starvation. Or they might end up on a plate: they taste good to people as well as lions.

Fifty thousand people have signed a petition to save Marius II. I'm one of them. And, if every signatory gave a couple of quid, there would be enough money for a suitably accredited zoo to build a new giraffe house. Joe Public will also have to man up to this debate. There will always come a time when you have one too many animals. And what do you do then?

Benjamin Mee is a writer who rescued Dartmoor Zoological Park