Here is a quick down and dirty VBS script that will disconnect the kit.
first part makes sure the main SGP window is the focus, then it sends ctrl-shift-D to disconnect. then it makes the yes/no window the focus and sends enter for yes.
Set objShell = WScript.CreateObject("WScript.Shell")
objShell.AppActivate("Sequence Generator Pro")
objShell.SendKeys "^+d"
Wscript.sleep 3000
objShell.AppActivate("Disconnect")
objShell.SendKeys "~"