I mean it's a disadvantage to the person trying to reap the benefits of the spell. For the cleric casting the spell, on occasion it can be an advantage, sometimes it can be a disadvantage, most often it never comes into play.
Read the Old Testament, for example. If your god likes you and doesn't like your enemy, that tough for him. If you've been a jerk-off to your own god, and expect a favor from him, likewise, tough luck.
I suppose it could also depend on the god... Some are more aloof toward their worshippers than others.
In the end, however, it is another valid means to arbitrate the dilemma.