The long and short of it, the real reason such controversy exist in our current state is because the nature of the church and state argument has been perverted from its intent.
The original intention of the church and state argument was to prevent a federal sponsored church from being established, that's all it was. It was not to keep government and religion separate. There was no rule against public prayer, not for any religion. For crying out loud, congress printed and issued an official congressional bible to each freshman member until the 1930's.
Here's the simple solution, prayer is freedom of expression, if you don't like it then it's simple, just don't listen, don't pay attention. Every last one of us has been to some function, some event where we were either bored or uninterested, what did we do in those cases, we didn't pay attention, we didn't listen, we probably daydreamed...someone was speaking but during your little daydream I seriously doubt you heard one single word being said. It's not that hard, if you don't like it don't listen but to scoff and bitch about freedom of expression, which prayer is, well that's nothing short of ultimate stupidity and nothing short of bitching just to bitch. What are those that don't like the prayer worried about? Are they worried if they're in the same room that their ears might fall off due to prayer induced leprosy?