I'm not sure I understand the "problem" (perhaps "thought experiment" is a better term?).
Should a sidearm do no damage whatsoever to a starship?
First of all, you're meant to round down unless otherwise stated. That's on page 5, so no, a laser pistol cannot damage a free trader with armour 2.
Let's say I fire at a ship that is UNARMOURED.... well.... it's unarmoured? Imagine shooting any unarmoured vehicle. Most conventional weaponry is going to have at least a chance to punch through. And if I can punch thought the unarmoured hull, I can score a critical hit on some vital system, like puncturing a fuel tank, or hitting the engine.
Guns work by sending a small projectile of energy or metal or super heated plasma at a very high velocity..... they hurt people easily enough so I don't see why they shouldn't be able to damage a ship.
As for the empress marava class - it's a trading vessel..... You'd quite rightly do 2 points of damage and critically hit some ship system. If you donned vac-suits, opened up your air-lock and started firing a gauss rifle at it you'd probably cut it to ribbons. If the Marava class's twin double turrets don't vaporise you first....