Well, you're right about the topside thingy... I do believe that the turret-like things on the deck are Laser batteries (therefore they wouldn't need a long barrel). Also, the section of deck immediately aft of them looks like it comes open, and could possibly be a VLS (vertical launching system) for cruise missiles..... Of course, since you never actually see the ship fight during the game, this is all conjecture, but it does have military capabilities, since the captain mentions about preparing to fight the Galbadian Fleet, when the Estar fleet came and took Ellone, and the Galbadians chased after the Estari instead.....
As for Solid snake, give him stats about equal to a TOW infantry, but also give him stealth attack, invisible, treats all terrain as roads, zone of control, bombardment, radar, and amphibious attack, and he might just have a chance against the uber powerful Metal Gears.....