Congress shall make no law ...
That's all well and good - and I agree with it - but what does it have to do with a School Board? It doesn't say anything about a School Board establishing a religion..
The School Board is a part of - or at least, derives it authority from - the state (municipalities do not exist under the Constitution; their powers are derived from the state). So the real question is, does the first amendment's establishment clause apply to the states as it does to the federal government? The answer is that the Supreme Court has held that first article of the fourteenth amendment compels states to comply with most of the Bill of Rights (relevent text in bold):
All persons born or naturalized in the United States, and subject to the jurisdiction thereof, are citizens of the United States and of the State wherein they reside. No State shall make or enforce any law which shall abridge the privileges or immunities of citizens of the United States; nor shall any State deprive any person of life, liberty, or property, without due process of law; nor deny to any person within its jurisdiction the equal protection of the laws.
So most of the Bill of Rights applies to states, including the First Amendment. The establishment clause therefore restricts the School Board from establishing a religion, which the courts have held can include teaching religiously-influenced non-science in a science class. (That is, until the majority on our conservative supreme court - they of "strict constructivism" - decide to pass an entirely new law taken from their collective rectum.)