Read on for Apple's recommend procedure for removing Classic...
This is taken verbatim (except for some formatting changes) from page 32 of the above-linked PDF...
Warning: Incorrectly entering any of the commands described in this task can erase critical data. Pay particular attention to correctly entering single quotes. Misplacing these single quotes can result in the removal of Mac OS X or applications.
To remove Mac OS 9 and Mac OS 9 applications and files:
- Log in to Mac OS X as an administrator who can use sudo to remove files. By default, all users who are administrators can use the sudo command to remove files. If you modify /etc/sudoers, you can choose which users can use sudo. For information about how to modify the /etc/sudoers file, enter man sudoers in a Terminal window.
- Open Terminal.
- Enter the following command to remove the Classic icon from System Preferences:
$ sudo srm –rf '/System/Library/PreferencePanes/Classic.prefPane' - Enter the following commands to remove Classic folders and files:
$ sudo srm –rf '/System/Library/Classic/' $ sudo srm –rf '/System/Library/CoreServices/Classic Startup.app' $ sudo srm –rf \ '/System/Library/UserTemplate/English.lproj/Desktop/Desktop (Mac OS 9)' - Enter the following commands to remove Mac OS 9 folders and files:
$ sudo srm –rf '/System Folder' $ sudo srm –rf '/Mac OS 9 Files/' - Enter the following command to remove Mac OS 9 applications:
sudo srm –rf '/Applications (Mac OS 9)' - Restart the computer.

