I want to take it out of operation permanently and safely
Put a black tape on it
The question would be whether drilling was the method of choice; I would rather use an adhesive tape or something similar. Recommend to remove as clean as possible in case of doubt ;-)
Drill out?
How come?
Simply stick an adhesive strip on the lens and no one can see anything.
Must be gone permanently!
I doubt you can do that by drilling out. You can probably throw away your whole laptop right away.
Then - who would have thought - you no longer have a functional camera. It may also break more at the same time. Masking or uninstalling the driver would probably be a better alternative.
What kind of laptop is it?
You can remove it without damaging the housing.