I think you're concerned about a fatigue failure at the corners of the holes in the cranks (where there's a stress riser)? Well designed cranks have fillets between the flats and should take thousands of on-off cycles to elongate micro-cracks enough to pose any danger.
I would be more concerned about the installation/ removal procedure scratching the crank which might start a macro crack. Cleaning then re-greasing or using anti seize should minimize that worry.
http://en.wikipedia.org/wiki/Fatigue_(material)
If anything, I'd think the crank threads for the remover tool would be the weak link.