Sometimes you need to uninstall Kojo to upgrade to a newer version (this happens when jar names in the Kojo lib directory change). Doing so is easy.
use Start Menu -> All Programs -> Kojo v2 -> Uninstall Kojo
Go into ~/Kojo2/Uninstaller and run ./uninstall-kojo
After you're done uninstalling, you can also delete the Kojo install directory for good measure.
The only real difference between running the uninstaller and just deleting the install directory is that the uninstaller gets rid of Desktop shortcuts and (on Windows) the Start Menu entries.