You’re right that the New York Times ran the headline ‘God is Dead’ (note that the headline includes the single-quotation marks), but it’s above a paragraph that reads
This is followed by the text of the ritual. So it wasn’t the Times saying “God is dead” but instead a religious school that did so, as an exploration of theology.
What? Really?! What were these people expecting the Times to tell them? “Yes, this has been confirmed. Police suspect foul play; apparently, someone shot Him in Reno just to watch Him die. The funeral is next Tuesday at noon.”