There is no easy way to implement DragDrop between Silverlight applications and I am not sure if there is an acceptable solution at all.
If you go for the single Silverlight application, then you will still have problems with the mouse events because any Html overlay will capture them. Also here you will not be able to have popups above the Html content, so the DragCue, any menus and DropDowns would not work as expected.
In short, even if you manage to implement a kind of drag-drop between Silverlight applications then this will possibly be "hacky" and fragile. Unfortunately I cannot think of any solution that I can recommend.
the Telerik team