Well, lets clear up a few things. Usually LR is not collected directly from a reef, it is usually collected in the "rubble" zone between the reef and the shore for many reasons, key among those being that it's much easier to dive and collect there

. So our collection is not really hindering reefs per-say, just the reef's dumping ground. Also while perhaps not sustainable, LR collection does fall under CITES regulations so its collection and impact on the environment is monitored and controlled. Not just anyone can go get this stuff.
Now the other half of the issue is what to do about it. Well, there are a few LR suppliers here in the states that actually Aquaculture or "grow" LR. Tampabaysaltwater.com was the first to do so if memory serves and is still a big outfit, but a few others have sprung up after TBSW's success. What these firms do is purchase rubble from tropical construction sites which would otherwise have been discarded. Almost all rubble from digging in truly tropical areas of the carribean is dead live rock. Most of the carribean isles were reefs millions of years ago, so when you dig up "stone" there you get dead LR. So these aquaculture firms then get permits from the appropriate agency, rent a barge, take it off the coast of south florida in between the reef and the shore, and create their own rubble zone. They leave the rock for a year or more and then start diving and collecting on their site. The really nice part about doing LR this way is that because the whole operation is man-made and aquacultured, CITES restrictions do not apply and rock can be shipped with all kinds of extra goodies. Shrimp, clams, corals, sea fans, etc are in excessive abundance on this "man made" rock. Fantastic stuff, and expensive...
Perhaps someday all LR will be created/collected this way