There have been pirates since there has been commercial maritime activity. Contrary to apparent popular opinion, our "pirate problem" has never gone away. Piracy has existed, and continued to exist LONG after the Barbary Wars, even in those very same waters.
I don't think you realize what the size of the body of water we're talking about is. The pirates operate far beyond literal waters, extending their reach to an area that far surpasses the size of the United States. Our Navy is just not that big.
No one is saying that pirates shouldn't be dealt with harshly, but to opine that we're going to sacrifice the hostages in the name of the greater good, is farcical. Pirates are criminals. There is a role for us federal police agencies, like the FBI hear, especially when there's an active-hostage crisis.