Two ways.
One)
From your server console, or game console if you run a remote server use rcon , "remove <the_steam:id:you:wish_to_remove>" , then "writeid" to write it to the file permanently.
OR
Two)
Open up your gmod/cfg/banned_user.cfg using notepad, find the users steam id you want removed, remove its entire 'banid # <steam:id>" line
Save the file, (re)start your server.
[edit] Syntax correction
