I think there are a lot of angles to this issue. The first would be the destruction of wild habitats/depletion of wild populations. This tends to be more of a marine/reef issue then a freshwater issue, but can't be ignored because of that. Also, I believe it's less of a problem then it used to be, as I think damaging capture methods like dynamiting and cyanide were already on the decline a decade or more ago.
On the other hand, the damage the aqarium trade does to reefs is going to me negligible (as stated above) compared to the effects of climate change. rising ocean temps, increasing acidity, there is already a great loss of coral due to bleaching in some areas, and it's just going to get worse.
Overfishing for the seafood industry, while primarily targeting different environs, will also do far more damage to the ocean ecosystems then our hobby.
But our hobby is insignificantly small compared to the seafood industry, or the corporations that want to block any sort of talk about carbon emissions.
Another issue (also stated above) is the issue with releasing non-native species (or even captive raised native species, to a lesser extent). This doesn't just affect the aquarium hobby, it's a pretty big issue wit a lot of herp stuff as well. I'm sure you've all seen the pictures of the dead constrictor that swallowed an alligator and ruptured. Apparently this is becoming a problem in Florida, since the habitat is suits them pretty well.
As Bermyguy pointed out, the lionfish example wasn't due to hobbyists, but we are still going to get the blame. Many other introduction of non-native species are actually intentional acts done by the government under various conservation (and conservation is very different from environmental protection) issues. But hobbyists will get the blame; and sometimes we deserve it, I've known too many people who when they get tired of taking care of a critter, take it outside and let it go. I believe that's whey the Western Pond Turtle is in trouble out here in CA, the red-ear sliders (typical baby turtle) are competing with them. We need to make sure that we are careful not to accidentally (or intentionally) release captive critters into the wild, and do our best to educate others not to release them as well.