The Golden Throne as irreparable is the easy part. It slowly breaks down over the next few decades/centuries/millenia. The game won't last that long.
I've been wondering if the creators (if they still have control, I don't know) are simply retiring and looking for a way out without giving up their baby, and want to do like another game company did and just destroy their creation in a giant apocalypse. I mean, how long will Warhammer go on? Will it outlive its creators? Who would inherit the rights? Do they want to administer a genre estate?
I wouldn't mind a reset scenario where humanity is broken into a bunch of little empires. Of course, that means they'd have to tone down some of the uber-badness of the Imperium's many enemies, and a general apocalypse might do that very well indeed.
An easy wrap up, or perhaps re-boot, would be to actually kill the Emperor. Let the psychic death rattle kill billions of astropaths and navigators - grinding interstellar communication and transportation nigh impossible. The Imperium of would fracture into tiny pocket Imperiums. This would allow essentially a soft reboot because you could simply advance the timeline 5-10 millennia with nary more than a hand-wave. Welcome to Warhammer 50K, *******... buy our new models.
When the story picks back up, GW could literally write a new universe.