I thought the Navy handled this incident brilliantly. To their credit they did attempt to negotiate until they felt they had no other option and the CO of the Bainbridge made a decision that had already been authorized by the President.
Handling further incidents unfortunately has to be done case by case. I don't think there can be a blanket policy here because there are so many different factors. The sheer vastness of the body of water the military is being asked to patrol makes it impossible for them to be everywhere at once. The involvment of hostages makes every interception difficult because if innocents start getting killed in rescue attempts it would be impractical to continue such attempts. Finally as has been pointed out taking the fight to the pirates, while already authorized by the UN, is difficult because they do blend in with the locals so well and any action could be met with reprisal on the Somali people which no one wants to see.
At some point though I would guess that all these factors has to be weighed against the cost of allowing the pirates to continue on their present course of action.
"You'll find that many of the truths we cling to depend greatly on our own point of view."