A worthy question to ask would be if the Founding Fathers understood the term religion in the same sense as us. It is well-known that the Founding Fathers were tolerant of Deism, and in fact included a few Deists. However, Deism doesn't come with any set of commandments, no doctrines, no holidays that have to be celebrated, no services and makes no comment on the afterlife. Essentially, it's a minimalistic version of intelligent design: The Universe originated through some intelligent agent. Period.
Is this really what we would consider a religion? Perhaps not. However, seeing we don't hear Thomas Paine complaining loudly about how the Deists were treated unfairly in the wording of the First Amendment, all we can conclude is that the Founding Fathers understood the First Amendment to give a perfect defense of Deism.
As such, one may very well begin to wonder if the Founding Fathers' definition of religion wouldn't actually be more closer in line with theological philosophy in the terminology of today. If so, then the First Amendment does actually already provide a perfect and full defense of Atheism.