Siege Destroyer was originally planned for release with JA, but scrapped at the last minute due to lack of time.
A lot of REMNANTS of this scenario are left in the game's code, which people quickly enabled through cheats and tweaks.
You could always use vehicles (X-Wing, Z95, TIE Bomber, TIE Bomber2, TIE Fighter, Lambda Shuttle, Swoops, AT-ST), but the ships were left out on purpose (cheats only) for this reason.
Fast Forward a year, and Raven (with the help of some guys from the community) polished up Siege Destroyer and released it unofficially for the community for free.
This was the map pretty much "as is" except they had removed the "inside the ship" scenario that was never really what they wanted and fixed some of the bugs and made it playable. It had features not seen in anything like KOTOR before like ship targetting, radar that showed more than just friendly ships, free floating destroyable asteroids, hyperspace warping, etc.
It features four ships, all ones that could be used in the game with cheats previously.
Of course this wasn't the end.
A little while later this same team released ASTEROIDS which is a mod that adds four more flyable ships (TIE Advanced, TIE Interceptor, A-Wing, Y-Wing) along with a TON of tweaks, fixes and things. Ship handling is greatly improved over the ships in the base game.
As an added bonus ASTEROIDS included a NEW REVAMPED version of Siege Destroyer (Star Destroyer Attack 2.0) which included all the features and fixes of Asteroids plus balanced for the new ships (and including a Shuttle for the Imperials) and a more challenging mission (8 minutes to win instead of 20).
Through cheats you can use a tweaked version of the YT-1300 as well. While still buggy and unbalanced, the ship is a lot easier to use and more useful than it was just using the tweaks some people had released previously.
Trust me, playing with vehicles spawned in through cheats and playing this are worlds apart.
Grab Asteroids here, it's what ship combat was INTENDED TO BE in Jedi Academy all along.
http://www.lucasfiles.com/index.php?s=&action=file&id=464)