But why? You aren't a Republic/Sith Admiral trying to assault Coruscant, you are just a small band of galaxy saviours/conquerers. So why would you go clunking around in a capital ship, especially if most of the time you are trying to keep a low profile? Besides, it is completely
away from the style of the other games- it just doesn't fit in KotOR. We aren't playing Empire at War, you know.
Just like The Doctor wisely said: The Hawk is part of KotOR, if not all of Star Wars. Luke didn't go zooming around in a super star destroyer, did he? Of course, Darth Vader did. But in that case, perhaps near the end of the game, if you have taken over the Sith as Darth someone you could have a capital ship. But for all of us others, who would be alienated from the game, the Hawk needs to be there. Even if you could destroy it if you really want- it just needs to be in there, at least as an option.
As far as making it work, droids cost money. As does a capital ship. As does programs designed to keep the droids running. Add this to repairs, to damage from pirates and Sith warships all coming to attack your huge and very obvious ship- you better have a lot of money. Come on, you obviously aren't going to start the game with a capital ship, are you? And not given to you either, that would just be stupid.