To merge the objects remaining in the namespace to the parent or root namespace, use flags mergeNamespaceWithParent or mergeNamespaceWithRoot. The empty file reference namespace is then removed. To forcibly delete all objects, use flag force. The empty file reference namespace is then removed.
from http://help.autodesk.com/cloudhelp/2016/ENU/Maya-Tech-Docs/PyMel/generated/classes/pymel.core.system/pymel.core.system.FileReference.html#pymel.core.system.FileReference.remove
These flags are not available when calling the remove() method. (Tested with
pm.FileReference(reference_node).remove(force=True)
)