I kill the skype task using: taskkill /f /im lync.exe and I see Skype close and the task disappear 
I run the command line for the office deployment tool using the above XML: 
setup.exe /configure RemoveSkype.xml
I kill the skype task using: taskkill /f /im lync.exe and I see Skype close and the task disappear 
I run the command line for the office deployment tool using the above XML: 
setup.exe /configure RemoveSkype.xml