Send them an expensive bill, they will learn i the end
Is there a way to enable trough the code some protection measure like shutting down the Atmega after a certain period of time? Or ending the sketch? Or entering in some kind of safe mode?
yes, yes, no but I doubt if that is what you need (all disclaimers apply)
Your requirements are too unclear to give definitive answers especially for commercial projects - incomplete and wrong answers costs money too you know
So tell us more about what you want to protect. (and remember there is no 100% protection ever)
The expensive bill scenario is not really an option.

In fact I am a little embarrassed even though the unit breaks down when used in conditions that have nothing to do with normal use. I was hoping I made something fool proof.
It's a sort of ballistic chronograph for slowish projectiles, not bullets . The problem appears when it is accidentally left ON for many hours or even days (weekend). People forget to turn them OFF. When the Arduino is turned on, the chronograph starts automatically. If it's not stopped it keeps working. Somehow this does something to the Atmega and the unit won't work. If I reinstall the sketch, it works fine.
I don't really know what is happening with the sketch. I don't know if the problem is the actual time the unit is turned ON or the fact that the battery drains out and after some hours the voltage drops so much that it messes up the Atmega.
I am looking for a way to stop everything after let's say 2 minutes of not being used.