I am sorry for the confusion on this. While the standalone Test Studio IDE is (mostly) autonomous, as soon as you want to integrate it with TFS source control, you add a dependency on TFS components and the way TFS source control works. For starters Test Studio does not come with the TFS DLL's required to connect to a TFS source control repository (I think you already know this) because Microsoft doesn't allow redistribution of their DLL's. You must at least install the Microsoft Team Explorer (which comes with Visual Studio). Second the source control and the workspaces are TFS controlled, not Test Studio controlled. Test Studio is a user and consumer of them, not the controller of them.
Also, Test Studio is not, and never will be, a full fledged workspace manager or source control manager. The product is not intended to be such. It is only a TFS source control client intended to use TFS source control but nothing beyond that.
When there is a problem with the workspace (such as you are experiencing) or the source code repository you must use a Microsoft tool to make the required adjustment. Test Studio does not include the ability to make these types of adjustments to your TFS controlled source code repository or TFS controlled workspace.
I hope this explanation clears up any misunderstanding how the two work together.