Just becuase its the size of planets and its covered in loads of turrets, and just becuase its got the firepower to level whole fleets in one good shot, doesent mean its unstopable.
In fact, i could probably have in down in three missions:
1) Use Stealth fighters to take out turrets while a destroyer or two provides a distraction. Then go for engines to prevent escape.
2) Surround area with warfleet to take out anything which tries to save the Gargant.
3) Send LOADS and LOADS of bombers, with LOADS and LOADS of capital ship support, to blast the ship right back to the stone age.
Though that's not to say that the Gargant is weak. In fact, i bet it could send the Colossus packing in one good broadside.