I know I said I would have something today but i got sidetracked playing planetside 2 with some friends. Tomorrow!
I would probably agree on a saboteur, as it is incredibly hard for any one thing to knock a star destroyer of that size out of the sky. Maybe he/she would destroy the engines whilst in hyperspace, sending the vessel careening into a planet, etc.
Well, I am open to suggestions. There's always the good ol' EMP's.
Maybe there's some large EMP field around one of the planets? Then some rebels come and shoot us down while we're EMP'd? Maybe something happens to the life support and we have to go down to the planet? Just kinda throwing some ideas out there.
@Azkott Maybe the rebels have taken hold of an ancient artifact. A giant pyramid that can shoot a golden yellow laser with special properties. The only downside is that it has a short reach, still enough to take down our ship that just so happened to pass near it.