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?
Your two questions are very important! Seems to me, the free speech environment is what the framers had in mind.
IMHO, the key will be whether and in what circumstances the Supremes hold that atheism is a religion.
Oh, I'd expect such an environment would ultimately conduce to what we see in George Orwell's Animal Farm. There was a whole lot of lip service paid to tolerance and equality in those pages; but in the end, some animals were "more equal than others."
(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?
I imagine it would look like a civilized society. Free speech, freedom of conscience (religious liberty) are essential to check the libido dominandi of would-be tyrants seeking to amass and consolidate sociopolitical power in their own hands.
FWIW. You ask such great questions, xzins!!! These would be my answers, off the top of my head. Other people's answers will likely differ.