If you really need to get rid of these files, boot into Safe Mode, and delete them from there.
Perhaps a tool such as "MoveOnBoot" could be of help ?
(also if files and folders are marked as "read only" then it might be a good idea to start with altering folder and file properties so that they are not "readonly" anymore ; right-click on folder choose "properties" , then set "properties")
As far as I know then the "Windows Installer Cleanup tool" do not remove the files themselves but only the installer files and registry information (to put it short : then you'll get the program of your list of installed programs but it leaves the program-files) .
For reference please see the link given to the "Windows Installer Cleanup tool" by Appligent : http://support.microsoft.com/kb/290301
look at the bottom at the page where it is suggested that one re-installs the program in the same folder not to have the files more than once on ones harddrive !