I use SSH to gain access to my Windows 2000 command line, so that will be reflected in the below steps.
Step #1: Connect to the server if you are not sitting at it
ssh username@win2000server -i privatekey
Step #2: Find out which sessions are currently active
query session
SESSIONNAME USERNAME ID STATE TYPE DEVICE
>console 0 Conn wdcon
rdp-tcp 65536 Listen rdpwd
rdp-tcp
Step #3: We want to kill the connection with an ID of 1 (we can tell by the username and that it is active)
tsdiscon 1 /v
Disconnecting sessionID 1 from sessionname RDP-Tcp
That's it :) Easy eh?