Regardless of whose waters the ship was in, and legal nipickings, the Captin was being eminantly sensible.

There are heavily armed Israli warships, which have come under fire. Do you, responsible for the ship and the people you are evacuating, steam on in without thinking, "full speed ahead and damn the torpedoes!" style? Or do you make contact with the more powerful millitary force, and generally take all reasonable measure to make sure you're not at the wrong end of an anti-ship missile or two, even if they have no legal right to control navigation in those waters?

I'd rather be cautious, polite, and safer.