Oh good, more absurdly terrible sensationalized reporting. Here are a few more quotes from his speech:
"No principle of democracy is more fundamental than what has become known as the separation of church and state."
“It would be wrong to think, however, that the separation of church and state must mean that the political views of men and women must not be informed by their religious beliefs."
I haven't been able to find a full transcript, but the gist of it seems to be no different than anything he's said for the past 30 years: people are free to practice whatever religion they wish (or none at all) without government interference, but it's acceptable for the government to recognize religion through things like Christmas tree displays, prayers before legislative sessions, voluntary school prayer, statues of religious figures, etc. I rarely agree with his religious rulings and I suspect that he might feel differently if the dominant religion were one other than his own, but his beliefs really aren't that outrageous or dangerous.
From what I can tell, the "favor religion over non-religion" part just meant that he believes it's appropriate for government employees to talk about religion even while serving in an official capacity. He contrasted this to countries that enforce secularism by banning government officials from referring to their religious beliefs.
But I haven't read the whole speech, so maybe it really was part of his master plan to send atheists to death camps.