I think that for the heretics, the whole point of hunting for old and mysterious weapons is in fact about having something powerful enough to kill the Emperor. The leaders of the rebellion must know that the Emperor is a perpetual and cannot be killed with "standard" weapons, but they also know that there are weapons capable of killing such individuals, one of which is introduced in Vulkan Lives. The fact that Erebus helps John Grammaticus to get away, knowing (and probably hoping) that he will kill Vulkan with the Fulgurite shows that the Heretics know about the perpetuals, and know how to kill them.
So, to get back to the subject, I think that during the duel, the Emperor was wounded mortally by Horus with such a weapon, and that the only option left to the loyalists was to sit Him on the Golden Throne, knowing that his inevitable death would tear the Imperium appart as sure as any Heresy. This would stick to the story even if the Emperor wasn't a perpetual, but "only" an immortal. I don't really believe in him getting up from his Throne, because if he could have recovered from his wounds he would have been able to do it a number of times during his travel from Horus' flagship to the Golden Throne.
And if I remember well, his immortality is mentionned in an older book of the series (A Thousand Sons or The Outcast Dead).
Last edited by Kaminsky; 01-09-14 at 07:03 PM.