Maybe the station has some protection against that?
Was it close to a planet? Maybe that inhibits the ability to fly in hyper space too close?
Being that it's Clone Wars, a lot of it is ill-conceived IMO.
In X-Wing the Alliance steals a shuttle and delivers an explosive to a Destroyer hidden amongst the stolen shuttle's original cargo. It's one of the first, or an early anyway, destruction of a Destroyer I guess.
Anyway, basically, it was a billion times more plausible than this whole arc, and it was a 30 second cut scene in a game from the 1990's.
Another scenario had them taking a Corvette, setting it to autopilot a course at an Imperial Drydock that would have it basically ram through the command towers of destroyer after destroyer that were docked for repairs, and ruin operations for a sector. A similarly awesome sabotage scenario.
I highly suggest anyone interested look those cutscenes up on Youtube. They're short, glorious, and you got to actually be a part of it all if you played the game to boot. That's just good fun.