What is this US merchant fleet of which you speak? There is no such thing as far as I know. There are USN fleet vessels that are cargo carriers. There are some private owned US flagged vessels, though not many. Then there are thousands of vessels that are cargo carriers but not US flagged. The only ones that the government can command to go anywhere are the USN, which is what is in place.
We have prepositioned ships worldwide with either war material or "port-opening" packages in case a war breaks out here and there. We also have government owned-civilian contracted vessels that are sitting stateside rusting in Reduced Operating Status without any current cargo or mission. Most of the cargo work in the war on terror currently is being carried out by commercial carriers, as they get first dibs on the cargo lifts.
What the world truly needs are prepositioned cargo ships that can down-load "Disaster relief/humanitarian" packages ("port opening" packages) of mechanical handling equipment, container handlers, bull dozers, back hoes, front end loaders, some military escort command & control vehicles, portable field kitchens, ambulances, hospital units, medicines, graves registration units, containers of emergency food and water rations, generators, etc. This is definitely doable. It's just who is going to pay for it all? It might as well be us, because we end up giving a blank check to the country in dire need anyway.
In the future, we can tweak (de-militarize) some of our military cargo load-outs aboard the prepositioned ships with "port-opening" packages so that it can be used for either a military mission or a humanitarian mission. A single ship of either the Watson-class or Bob Hope-class of LMSR can haul 390,000 square feet of cargo at 24 knots over 10,000 miles (further, if you cut back on the speed). The ship could team up with an aircraft carrier and work the problem with the addition of helocopter transport. That's a lot better than the current situation of having a single carrier being able to steam at 50+ knots and not much else to show for it...(The Firstest with the Leastest). Natural disasters are going to happen (especially if you buy into Global Warming). We should be better prepared to help ourselves as well as others...this stuff is all off-the-shelf technology.
Preposition one of these Disaster Rapid Response ships in Puerto Rico,for example, and as a Hurricane moves in, or Volcano blows, or earthquake occurs...move the ship around to allow for a quick transit to the nearest useable port and facilitate a rapid off-load to cover the entire Carribean and Gulf of Mexico. The Comms and control suite will be kept ready to roll aboard the ship and manned-up quickly as the disaster occurs (The disaster Command & Control staff/liason team can be put aboard by helo if underway). Allow redundancy for 2 or 3 possible drop-off points to cover a larger area or disaster of greater magnitude. Include in the Command & control staff personnel to liason with whatever hospital ship is to be sent to the area.
Imagine how a prepositioned Disaster Relief/ humanitarian-aid ship will make whatever administration is in power look to the rest of the world...Oh wait a minute...this makes too much sense...It'll Never Work...