I can only think of two options to display notifications while trying not to obscure a user's workspace:
a.) Don't display notifications in the working area (e.g. display them in the panel, Android-style)
b.) Resize the working area to allow the notification to display (e.g. slide up from the bottom resizing all open windows - potentially jarring)
If we are accepting we must obscure the user's working area (which isn't really ideal) we should allow the user to either configure the notifications so they don't interrupt their specific workflow, allow them to be closed (still not ideal; interrupting flow), or just be a little arrogant about it and if they don't like it they can remove them (current approach).
Luke.