You do not need to use WebMatrix at all; another option is to simply upload files from FTP, and then create a VS solution and add the files you downloaded.
From Visual Studio, you can easily deploy the solution for TFS on your azure website.
As an additional note, from today (January 28, 2014) registry editing proposed by SilverNinja is no longer required, I was able to open VS 2013 Professional from Webmatrix without editing the registry.
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