I'd rather have these cheetahs in captivity even if they're being "domesticated" than have none in the wild! If we lose all the wild cheetahs, even if the captive group has lost some wild behaviors/diversity/whatever, it's better than having no cheetahs. This mostly sums up my view on all wild animals in captivity, really.
The so-called scientifically based article is based around an idea first and randomly picks out unrelated issues with captive cheetah husbandry and management practices in all captive - including non-accredited and petting institutions - locations which blots out the whys and wherefores and rationale for captive assurance and conservation breeding as a valid conservation measure. I will admit the petting zoos do not contribute in any way to conservation education, but the captive-breeding centers do make a significant contribution. Further aspects of wild cheetah ecology are thrown in to underline the "flawed" captive cheetah populations. It remains unclear on which studies they base various issues associated with captivity on cheetah breeding success, overall welfare and well-being. I thus consider this article pseudo science. If you are really looking for substantive information please look at the ICF in Namibia which I consider the world authority on cheetah ecology and conservation.