This article hits close to home as I do this sort of work for a living (help people/entities/government/etc. obtain permits to build marinas, docks, dredge, etc.). My company recently permitted dredging and a new docking facility for a huge, national company that contracts with the armed forces and the federal gevernment to build military items. I have a few things to say. Please note that I love reefs and I am only providing the information to inform people:
1. The project objective seems to be a matter of national security
2. Many local, state, and federal agenies review these type of applications. For the federal agencies, the national marine fisheries service, us army corps of engineers, fish and wildlife service, epa, noaa, and others review the application with microscopes. The permitting process would likely take more than 5 years to do something of this magnitude. During the permitting process, the corps is the lead agency, and they consult with the other agencies. the COE requires that the impacts to submerged resources (corals, seagrasses, etc.) be avoided as much as possible. Once the project has shown avoidance, the project must minimize impacts to the resources. Of course, avoidance and minimization is a very slippery slope since it is very objective. Of course the best way to avoid and minimize impacts is by not doing the project. However, the "no project alternative" is not considered an option. Once avoidance and minimization has been proved to the agencies satisfaction, the applicant would be required to mitigate for the impacts. Mitigation is usually required to be at a high ratio (3:1 for example) to account for time delay, etc. This means that if the project results in the loss of 50 acres of reef, the applicant would be required to create new reef on the order of 3:1 (creation of 150 acre reef). No project would ever be approved that would result in net loss of resources or overall harm the environment.
3. Dredging can be conducted without the dispersal of sediments. suction dredges do this all the time. I have no idea why they think dredging would silt over the adjacent reefs.
4. Many people (including me) buy corals. All corals were originally collected from the wild, resulting in a loss of coral from the reefs. If you want to help save the coral reefs, stop littering, reduce your water usage, reduce your carbon emissions, etc. and stop buying corals. I haven't heard anyone complain about the new australian corals that are all over the market. Sounds like they are clearing out the reefs in australia.
My boss and I always say that all of the easy projects have been permitted, and there will never be another power plant, airport, port, etc. permitted in the country, because everyone has a voice and has the right to be heard. Just remember that everyone is affected by every project in one way or another, good and bad.