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I think GW needs to further the story by declaring the Emperor dead, but make it interesting by saying that the Imperium discovered that he's been dead for hundreds of years (which was a deep dark secret known only to the high lords of terra) and that the golden throne is just a beacon through which thousands of psykers maintain the astronomican.
Have human morale bolstered by the fact that they've been keeping it together without the Emperor. They then make a patron saint of the Emperor and continue to worship him as their deity of war.