The lines you quote here are the final lines of the poem, and provide an example for exactly that which you are suggesting:  that the ship deserves a more noble death.  The poem was written after a proposition to break down the old, ailing frigate Constitution.  Old Ironsides, as the Constitution was affectionately known, was a warship; “her deck” was “once red with heroes’ blood,” yet now “The harpies of the shore shall pluck/The eagle of the sea!”  The ship has a reputation, and is glorious as an eagle, yet those men who decide her fate are beasts who care not for her history or her status.  It is a battle-scarred veteran, this ship, and Holmes is arguing in the poem that it deserves a dignified death – not just to be dismantled unceremoniously.  He laments that the heroic ship could not die in battle, proud and patriotic – she lived by the sword, and it is only right that she should die by the sword:

Oh, better that her shattered bulk
Should sink beneath the wave;
Her thunders shook the might deep,
And there should be her grave;

So, when he says “And give her to the god of storms/The lightning and the gale!” he is wishing that the ship could be sunk at sea in a storm, and could be buried there where she was of most use – away from the calm, well-attended waters of the harbor.  She should die an honorable death, ravaged yet preserved beneath the surface of the sea.  A death worthy of her reputation and honor.