I am not that far in the Jedi Knight story, but: The Planet Prison didn't destroy Planets, it only disabled fleets and prevented ships to enter and leave the planet. Also the Hammer Station was supposed to be destroyed they just failed to do so properly. And I also doubt that Revan said "Hey, could I get some troops, ships and Jedi to protect a Space Station where I will create Droids for a mass genocide? K, thanks!"