Shaf's experience as a Coastie might be instructive here (certainly more useful than my experience as a highly-trained Internetter), but there are myriad legal issues that come into the discussion when talking about armed civilian merchant ships.
Admiralty law is one of the most confusing things I've ever looked into. Shipping companies generally don't want to get into the trick bag of arming their crews. For one thing, they aren't a professional fighting force with a depth of force-on-force know-how. And in legal terms, having one of your crew shoot and kill a foreign national (even in international waters) is a trick bag that's tough to get out of, even if it's clearly a self-defense situation. Plus, many countries won't accept entry of a foreign-flagged merchant vessel if the crew is armed; without a controlling international authority, an armed merchant vessel is really just a pirate ship. You also have the matter of putting individual crewmen in a situation that they may or may not have had in mind when they decided to go to sea; the crew of the Alabama
, for example, have said in court documents that they were expecting to be at least 600 miles out to sea (per State Department notices) when they rounded the Horn, but the captain took them to within 300 miles (which still seems really far out to me, but whatevs). It's really not just a simple matter of giving the crew guns and telling them to have at it.
Also found out recently that pirates have attempted to commandeer the Alabama
three more times since the 2009 events depicted in the film. Yikes.
As to the SEALs, my understanding is that the negotiations were merely taking place as a stalling tactic. Once they arrived on-scene, it was just a matter of time before the pirates were vaporized; they really were laying on the fantail for the better part of three days waiting for that one magic moment when they had 'three green'. It was just a matter of whether or not they could get Phillips back alive in the process. I think the film does a decent job of conveying Captain Phillips' understanding of that; up until the Navy arrives he's pretty cool and mellow, but once the destroyer shows up he knows the clock is ticking, and he becomes much more jumpy and nervous and even attempts to escape. If the lifeboat got to 10-12 miles off the Somali coast, a SEAL Delivery Vehicle
would have been launched with a 4-man crew, 60 pounds of explosives would have been attached to the hull of the lifeboat, and it would have been sunk in international waters. (At least that would be my presumption in that situation.) The U.S. military are not cops. They're not there to negotiate.