Sorry, freedom of religion IS derived from Christianity whether you can see it or not. It has to do with the recognition of the individual's conscience in determining his own private relationship with God. That did come through Locke from Owen as I understand it...
I suspect that freedom of religion came more from the Enlightenment than the Restoration.
The Enlightenment showed us that we no longer have to kowtow to religion, and that, in western society at least, religion was no longer allowed to rule secular society.
Stripped of their ability to rule and establish a theocracy, various religions (and sects, denominations, etc.) were forced to fight it out among themselves. None was able to dominate as had been the case in the past.
That said, let me ask you a question: If you could, would you prohibit the Air Force Academy from setting aside that area for the wiccans, pagans, etc.?
Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.