Unfortunately, anywhere they would want to build it close to town it would definitely destroy some of the reef. It's just not deep enough for these big ships, especially during low tide, and they would have to remove a large portion of the reef. I've dove all over the reef by the ferry pier and it would be a shame to ruin the reef. It's the reefs with their abundance of sea life that make scuba diving in the area wonderful. This is why they mentioned working with the local dive shops and hoping to sink another ship as an artificial reef in an attempt to satisfy their complaints about loosing a great dive site to the development of a pier.
We're not talking about a small pier with a few pylons. This is a massive undertaking as they need to be able to dock 4 ships at a time. So more than likely, they're talking about not one, but 2 enormous piers that are capable of handling huge ships, which will definitely have a major impact on the environment.
As a long-time scuba diver, I always practice what we were taught in class; when diving, take nothing, leave nothing. We are only visitors on this wonderful planet and we have a certain responsibility to the land and sea we have been blessed with, for it cannot be replaced once it has been destroyed. Reefs are very slow growing and take thousands of years to develop and when they're gone, they're gone.
But as I said, I'm sure it'll get built because it's all about the money and that's more important than preserving the reef. And that, my friends, is a very sad state of affairs as we seem to have that same sentiment about most places on Mother Earth.