While reefkeeping isn't 'green' by any measure, there're things that can be done to limit the impact. Using your RODI waste to water a garden with, for example.
I'd disagree that it's the antithesis to conservation, because it actually places value on otherwise valueless resources. Interest in reefkeeping and ecotourism has lead to marked improvement of both the actual reefs and reef management practices, when people moved in to educate them and pay them (orders of magnitude) more for things like net-caught fish. The actual number of organisms that're removed from reefs, in <i>most</i> cases, is probably minimal enough that it doesn't have much impact on <i>most</i> populations of fish and inverts. There are, of course, exceptions, but aquacultured, tank-raised, and maricultured fish, inverts, and corals are all becoming much more common. And, for the educated consumer, more desireable: I'd much rather have a tank-bred or aquacultured fish or invert than wild-caught, 'cause it's much more likely to thrive in my tank and much less likely to carry the worst types of pests. And, of course, people will pay higher prices for those animals.
So, yes, we're removing a lot of creatures from the wild, but comparative to commercial fishing for food species, the numbers are tiny, and being reduced as aquarium husbandry advances. People -- at least in my experience -- are becoming more educated about care and husbandry practices, so creatures will have more of a chance to survive in their tanks. (Twenty years ago, who'd think of setting up a tank and leaving it to mature for six months just so they could have a mandarin?) And, bottom line, it makes people give a crap about reefs and ocean environments in general. So ... on the one hand, yes, the hobby does some damage, but on the other hand, I'd argue that it does more to preserve reef environments than to damage them. At worst, I'd say that it's pretty much a break-even.