The real news here is not that Antonin Scalia said this, but that it's the slightest bit controversial. But that's not something that happened overnight. The secular left and their media servants have spent decades pushing the idea that the establishment clause is about protecting the non-religious from maniacal Jesus freaks - especially the nightmare scenario in which the Jesus freaks get a job with any public entity and are guided in any decision by biblical principles.
Scalia is a man who actually knows about the founding of the nation and about the thinking behind it. He knows perfectly well that separation of church and state was to prevent the state developing an official state denomination that would be favored over others - as was (and still is, at least nominally) the case in Britain. It was never considered a constitutional imperative that believing in God, or saying so, or being guided by said belief, should be verboten among government officials.