If you use the brush tool in gimp, it is antialiased by default, contrary to the pencil, which is not antialiased (but that would make the line jagged even when looking at it in GIMP).
Also, Rodo is right, if your texture resolution is not high enough, you can get some jagged edges. You should increase the texture size (going from 2048 to 4096) or the size of the mapped part in you UV map (though that would also imply redoing your UV map which I wouldn't do if I were you). On a second thought, 2048 feels a little small for a capital ship so go ahead and increase it.