I think we need to put these articles into perspective. Neither are saying that clowns are getting wiped out only because of harvesting for the aquarium hobby.
"But before you start shedding tears for Nemo and his buddies, keep in mind that this request isn’t based on any evidence of a decline in the clownfish population. Instead, what has sparked concern is the deteriorating health of coral reefs as a result of climate change and growing ocean acidity."
And I have serious doubts about the validity of the first article:
"Parents whose children fell in love with Nemo at the cinema are seeking out the clown fish in ever greater numbers, leading to over-harvesting of wild specimens because captive breeding programs cannot cope with demand."
I don't think that Petco was selling only captive-bred clowns back in 2008 like they do now. But I think captive raised clowns can definitely keep up with the demand. I'm willing to bet that capture of wild caught clowns has gone down.
As I clown breeder, I believe that wild clowns need to be brought into captive breeding programs to freshen up the gene pool. There are several strains of clowns (including the one I am breeding) that need a "gene clean-up" due to excessive inbreeding.
However, I think the bigger problem is the removal of host anemones from the wild. As an anemone enthusiast, I'm torn because the anemone I am most passionate about -- S. gigantea (natural host of percs and occis) -- cannot be bred or propagated in captivity. The only species of hosting anemone that can be propagated with a high level of success are BTAs. There has been limited success with H. magnifica, but the recovery time of the propagated nem is a lot longer than that of a BTA.
Fortunately, many of the host anemones are simply too large (many over 24") to collect. It would be hypocritical of me to say that all nems should be left in the ocean, since I have one in my tank. Ultimately it's up to us to make wise purchasing decisions when thinking about buying a nem. I've made it a point to help as many people as I can specifically when it comes to S. gigantea, to make sure that it has the highest chance of survival, since that means one less dead nem, and one less pulled from the ocean.