Administrators generally like to manage end-user computers without the users seeing or knowing what's being done to their machines as otherwise users might interfere with or even block certain administrative tasks from being performed on their machines. While the Disk Cleanup utility Cleanmgr.exe doesn't itself allow you to run the tool in hidden mode, you can do this by using the Psexec.exe tool which can be downloaded for free from Windows Sysinternals, see http://technet.microsoft.com/en-us/sysinternals/bb897553.aspx. You can use Psexec to run Disk Cleanup in the background using the following command:
Psexec -s -d Cleanmgr.exe
Doing this will run Disk Cleanup on a non-interactive service window desktop that is hidden from the user.