I don't think it was a remotely tough call, but President Obama did the right thing in giving the green light to the Navy to use force against the pirates holding Captain Richard Phillips. He would have done the right thing even if the rescue had gone poorly. These decisions are made - and must be evaluated - before the fact.
One of the things that annoys me, though, in the reporting of these things is the phrase "shoot to kill." As a general matter, there is no other way that responders shoot in these circumstances. Police officers, for example, are trained to aim at an area that is immediately below the target's neck and up to his eyes. If you are hit there, you are not likely to make another move which is the point. Police shoot to stop - immediately. A corrollary of this is that the target is likely to die. Because of this, cops are trained to use lethal force only where there would be justification to kill the suspect.
Maybe Navy SEALS have more leeway. Their training is unbelievable and I have heard that trained snipers will sometimes try to take less than a lethal shot. But I can't imagine why you would do anything but take a head shot here. You had to immediately incapacitate these guys and, unfortunately, there is no other way to do that.
Another thing. While this may dissuade pirates from ever again accosting a vessel flying a US flag, the only way that piracy will be eliminated is if this is the universal response. No ransom. No negotiations. Death or prison. Every time.