When you upload an Arduino sketch, it is compiled, stored in the Edison and executed as a process named sketch.elf. You can check it with this command:
ps | grep sketch.elf
The sketch.elf is stored in /sketch directory. During the booting process the sketch.elf will be executed automatically. If there is no sketch.elf in the sketch directory the sketch won't be execute because there is no sketch to execute.
Since the sketch.elf is a process you can kill it as any other process. Regarding the ATmega question, there is no ATmega328 on the board.
I hope this answers your question.