Don't do that. The Steam version of Jedi Academy requires you launch
directly through Steam.
You need to go into your Steam library, right click on Star Wars Jedi Knight Jedi Academy in your library, select Properties, and under that first tab there should be an option called Set Launch Options.
When you run the game, it has to be through Steam, until the Launcher is back up and running. The MBII.bat file will not work.