Separation of Church and State

It can be argued that the Separation of Church and State cannot be found in the US Constitution.  At the same time, the Establishment Clause of the 1st Amendment is used by some as evidence that the founders wanted a line drawn in the sand between Church and State.

I'm not concerned whether this separation is in the Constitution or not, I still think it's a good idea and should be maintained for a couple reasons:

1) It keeps the State from dictating what a religion teaches and practices.
2) It prevents the State from becoming a Theocracy.

There are Christian Dominionist movements afoot to either establish fundamentalist Christianity as the state religion or to "prove" that this is a Christian nation.  If the latter can be done the former is inevitable.  If this truly is a Christian nation, then what is to stop legislation that reflects fundamentalist Christian teaching and belief?  And wouldn't that violate the 1st Amendment by establishing a theocracy?  An example will suffice.

There is a loud and powerful push to bring prayer back to public schools.  It's thought that children are not allowed to pray before a test or lunch or anytime.  Actually it's a civil rights violation to stop a child from praying if the child isn't distracting or interfering with teaching.  A child can pray or read a Bible anytime during the school day, but they are not forced to pray.  Would establishing school prayer force prayer upon children?  Would there be an opt-out for students who are atheist?  And from which religious tradition would the prayers come?  Christianity?  Judaism?  Islam?  Hinduism?  The majority religion of the school district? Would this then become an establishment of a religion by the State via public education?

Thoughts?