Tom, someone may have authorised those shots (I'm fairly sure of it myself,) but I'm not sure it would have been NCA.
As I recall, the Captain of a ship at sea is pretty much the last of the unlimited monarchs - any orders he gives to his crew he's got to answer for, not them. He's going to be the "man on the spot" for any decisions that need to be made, and he'll be the one that answers for them anyhow.
I'm more inclined to think the Captain set the RoEs for the SEALs to follow, and the SEAL that took the shots (damned good job, by the by!) was following the RoEs as established previously.
The Captain won't be held accountable, simply because it would be politically unsound to allow that to happen and would hurt the approval ratings of the Obama administration (nevermind the factoid that the SEAL was correct to take the shot. As far as I'm concerned, pirates at sea should be an endangered species with free tags issued and an unlimited bag, but I'm just cranky that way. I don't view them any different from terrorists - and I still want to know why we haven't turned SEAL Team SIX and SFOD-Delta loose on them worldwide yet...)