how do you disconnect an active user logged in to a box?
You are looking for a combination of the rwinsta and qwinsta commands.
first do qwinsta /SERVER:<server_name> to get a list of session ids then do rwinsta <session_id> /SERVER:<server_name>
It should also be noted you can use the /console (rdp client < 6.0 i believe) or /admin (rdp client > 6.0 i believe) to get in onto session 0 or the console session which should allow you to kick people from the gui.