You may recall an incident in July of last year in which a Navy oiler fired on an apparent fishing vessel approaching at high speed. The fishermen were killed and the incident caused severe diplomatic problems. Navy Times website has a writeup, here, that I encourage you to read. This is a classic no win situation. If the Navy ship doesn't shoot, it risks becoming the next USS Cole. If it shoots, it risks becoming the next USS Vincennes which is exactly what happended, albeit on a smaller scale.
I have no insight to offer other than the sad recognition of the conditions that terrorists have forced upon the world.