I think the larger amount of damage is done to the marine mammals, sea turtles, and other animals that are sensitive to sound waves.
The real damage isn't from the actual explosion per se, but from the massive sound wave which propagates far from the site underwater[1]. That assessment is discussing explosions much smaller than the one the Navy just did (and is scheduled to do twice again).
I'd like to believe to do something to mitigate the damage, but I don't know what they could possibly do for something this violent.