IMHO, there should be no ideological presupposition in a scientific investigation Nor should the gatekeepers force ideology on the evaluation of the results. If science would use Bohr's bar for an epistemic cut, we wouldn't be having this never-ending battle concerning intelligent design.
Both practices are also an affront to the First Amendment as xzins suggests - on the one hand establishing a religion - and on the other hand, preventing the free exercise of religion. Based on the current application of Lemon in public venues and the 7th ruling on atheism being religion, the Supreme Court is effectively establishing atheism as the state religion while preventing theism to be spoken in public.
Excellent points, AG.
To cover their prejudice these folks say that the prohibition of any expression is neutral, so therefore they cannot be charged with promoting atheism.
The questions to ask would be,
(1) what would a tolerant-but-atheist (or stealth-atheist for that matter) environment look like, and how does that compare with what we see in our own environment?
(2) what would a "free speech" environment look like, (since ultimately "free religion" would be covered by free speech)....and how would that look different than a tolerant-but-atheist environment?