There seems like no way to do this except for changing source code. In CollectGarbage method of LayoutRoot.cs, I commented out following code and got what I wanted - AvalonDock application without any DocumentPane. If there is really no method for this, I highly suggest the author have an option for this without modifying source. Hope it helps others like me.
if (emptyPane is LayoutDocumentPane &&
this.Descendents().OfType<LayoutDocumentPane>().Count(c => c != emptyPane) == 0)
continue;