Religion in Schools

The diminishing role of religion in our public lives has been criticized by many. A large portion of American society feels that the words "In God We Trust" are a cornerstone of American culture and life.
These statements may have the potential of insulting individuals of non-Christian faith and they may possibly limit their freedom, however, one has to consider that the United States as we know them today, were founded as a Christian nation.
Few foreigners would demand for all aspects of religion to be eliminated in an Arab or predominantly Catholic country.

In the U.S. News blog post Religion in Schools Debate Heats Up, two recent court cases are discussed regarding the role of religion in schools.
In Illinois, a judge ruled against state law, which bound students to observe a moment of silence, claiming the law violated the separation of church and state.

The Texas case involved biologists and social conservatives who tried to attain a ruling to limit instruction to the evolution theory and suppress any differing views or possible weaknesses of the evolution theory. The ruling is currently pending.

On the website of the Library of Congress one can view a letter written in 1935 to the school board of Minersville, PA. In the letter a parent explains that his son and daughter refused to salute the flag and pledge allegiance to the flag based on his religious beliefs as a Jehovah's witness.
As a consequence, the school board expelled the two children claiming insubordination.

Is either of the listed cases justified?
Should any sign of religion, be it the smallest religion-inspired thought, be banished from schools?
If so, should students be punished for expressing their religious beliefs while being at school?

One question follows the next.

I believe it is our duty to respect our historic heritage, which is the Christian faith, while providing ample opportunity and tolerance to help students explore the faiths of the world (one being atheism), which includes instruction in biology.
The scientists and non-Christians who foul and suspect officials to attempt to force a certain religion, try the very same with their forms of "religion:" atheism and nihilism.

On a side note: In Germany, religious symbols, such as crucifixes, have been banned from the classrooms, but German students still receive instruction in Christian religion, which is divided into Protestant and Catholic faiths. For students of non-Christian faiths a class in ethics is offered.