chdkptp has a gui mode as well - you can do everything you describe from there or via command line commands. No script needed.
Why do you need to stop the intervalometer script though? Can't you just transfer the pictures from the SD card while the script is running?
I like chdkptp a lot too, especially the live view function is great to see how the script is running on the camera.
Well, I can't transfer them while the script is running because when I connect the camera through USB, it goes automatically into PLAY mode.
This conversation is now spread across several threads, but I got the impression the OP wanted to leave cameras running an intervalometer script and just show up occasionally to download the images and clear the SD card.
waterwingz is right. I don't have a PC available which I can leave with the camera. It has to be stand alone.
I'm sorry for spreading the quest for my solution around different threads. But my situations actually involves different elements so it's not a bad thing I discuss the relevant topics in the correct threads.