To remove all source control from a TFS project (not a VS project!) - you must use the 'tf destroy' tool.
If, like me you try to delete the top-level directory/project node in Source Control Explorer (within VS), then you'll likely get the following error:
TF10169: Unsupported pending change attempted on team project folder $/MyProject. Use the Project Creation Wizard in Team Explorer to create a project or the Team Project deletion tool to delete one.
So, this (removing source control) is useful if you have a TFS project created just for project management assets eg Work Items, Sprints, PBI's etc.
Use the following syntax:
tf destroy $/<project name> /s:<server name>
eg:
tf destroy $/MyProject /s:mytfsserver.mydomain.com
The tf.exe tool is within the <Program Files>\Microsoft Visual Studio 9.0\VC dir.
Note that this will remove the project from the Source Control Explorer - but the TFS project still exists - you can see it in Team Explorer and/or TFS Web Access.