Simple: click the "hide" box only in Desktop folder
(In Windows Classic view)
Go to Windows Explorer; click on Desktop. Go to Tools/Folder Options. Click View, and check "Hide protected operating system files" - but, DO NOT CLICK "APPLY TO ALL FOLDERS". Just click OK.
Now, only the Desktop folder will hide the files but they will still show up in all other folders.
http://answers.microsoft.com/en-us/windows/forum/windows_7-desktop/hide-the-desktopini-from-the-desktop-view-while/56dcd199-c95a-427a-acf6-4eea66debaa8
