Well, it isn't any different to call her faith silly than it is for Bill or others to call not believing silly I would say. Now Perry's wife's behavior is silly in that she doesn't get that they aren't treated the way they are because they believe in God, but because of the way they act. All the presidents I know of have believed in God, so that isn't a big deal. It's how they behave about their beliefs that gets them treated how they have been and the victim mentality about the consequences of their behavior.
If a person ran on a platform of forcing all religious people to stop attending church the person would be attacked and rightfully so, just as the idea of forcing the Christian beliefs upon everyone gets attacked. She did seem pretty upset for so early in a campaign, and that isn't a good sign.