Once the ITCM Agent has uninstalled, the changes have already been made. You can either delete the registry values, to return the settings to their unconfigured defaults, or you can manually change them, to your desired setting.
For ITCM version 12.9 GA, there is testfix T55V141 (ITCM Uninstall Changes CTRL+ALT+) available. The testfix replaces ..\CA\DSM\bin\sxplgshl.dll. A function within this DLL file is called during uninstallation of the SD agent plugin, and is responsible for creating or setting the registry keys. After the fix is applied, the ITCM agent can be uninstalled, without these settings being affected.