You might want to post this in one of the software forums. You might get a better answer than mine.
I can point you in some direction but it will involve writing a script. Off the top of my head you can use the output of the "w" command to see how long the user has been idle. It will not be clean but for users that idle of a determined amount of time have the script "kill" the users process or login shell.
Be careful....I don't know what application you are looking to stop but there is always a chance that it might cause corruption or loss of data.
It is not the cleanest or prettiest.