Ok I know 2 options you can try (note I am using Windows ME I dont know directory paths I typed are the same for other OS, however they should be similiar.
1) Open the Control Panel folder, which you can access by press Start, then Settings, and in that folder click on Add/Remove Programs. Scroll down the list until you see JKII. Click on that and click uninstall. If this doesnt work or there is an error, then...
2) Go to Start, then Search, then click on For Files and Folders. Type in the first box Jedi Knight II: Jedi Outcast or whatever you named your JKII folder that contained all your files before you deleted it. Click Search, then wait until its done. Select all (or the files/folders you know are associated with the game JKII) and right-click, then press Delete. Click on Yes. You should be able to re-install now since everything that has to do with JKII is deleted from your HD (you know what I mean).