If the ISPF WSA component window is closed while ISPF is running in GUI mode, ISPF issues a 989 abend on the host, unless the "3270 mode after losing workstation connection" field is selected on the GUI Settings panel. If this field is selected, the GUI session continues in your 3270 emulator session.
If the GUI session has been ended and the Client/Server WSA component is no longer needed, the Workstation Agent window can be closed.