Although Boston Harbor is much less vulnerable then, say, New York Harbor or Long Island Sound, due to geographical and other factors (including Hull and Winthrop, which you are completely correct about), it is by no means invincible. That is where other factors, like the islands, come in.
The Harbor Islands do their part by ensuring that there is no direct outlet between the harbor and the ocean. You can't get from one to the other just by going in a straight line- some sort of land is in the way to act as a buffer in the rare event that more substantial storm surge gets past Hull and Winthrop, etc.
My point is, with sea levels rising and with storms becoming more intense, the Harbor Islands (all of them, not just Long Island) will become more important as a barrier island resource. Developing them substantially will destroy grasses, trees, and similar plants that hold soil in place on these islands. This will result in erosion and a reduction in the islands' ability to protect the city.
Even if it's (thankfully) not needed now, chances are it will be in the future. And I'd rather have as many resources to depend on as I possibly could. I'm not anti-development by any means, but when it comes to the Harbor Islands, minimal or no development is best.