I always used a sort of escalating strikes system, like each infraction last longer and longer. Behind the scenes of my games, I use the square of infraction times as time without your diety's favor.
First offense is one day without powers, second offense is four days, third is nine. If you can stay on the straight and narrow all that time even without your god's favor and attempt to make ammends for what you did, you can always eventually work your way back.
I never liked the idea of the atonement spell, always seemed insincere to me.