What I could suggest you is to try the ToolWindow that is in use in the Docking control. It has only the basic functionality of the RadWindow (drag and resize) and doesn't use any popups to display itself. That means that it shouldn't cause any problems to be in a control template, but you will need to add Popup to this control template and to put the ToolWindow in this Popup control.
Thank you for your comments - I'll write them down and will consider improving these things, but putting a RadWindow into a ControlTemplate is not a supported sceanario. May be we should consider creating simple window like the ToolWindow control that will not be in the Docking assembly and will allow you to do this.
the Telerik team