Worst case scenario:
No, but seriously, you can't damage the chip by programming it wrong. Not with the Arduino.
The worst you can do is set the fuses wrong (if the wrong chip is selected) and the sketch just won't run. All you're doing is programming flash. You can re-program it thousands of times. You could program it with just random junk and, while it won't do anything useful, it won't damage it.
You're far more likely to damage it by connecting things up wrong, or using wrong voltages, etc.