The MODS Editor probably should not allow the user to delete the root MODS element. It is debatable whether or not the editor really needs to show this element at all. When the mods element is deleted, the editor window cannot be restored (Since the EditorInput class uses the MODS ID as a reference).
The editor also allows the user to change the ID of the mods element, which leads to similar breakage.
The work around for both these issues is to not delete these values.
There is now an option to allow delete of the entire MODS record, via the menu on the div in the navigator.