Keep the pretender alive, albeit crippled, is probably better than letting him die of miasma (unless you decide to restart). At the very least, a living pretender helps maintain the dominion (ever notice how quick your dominion in provinces decline when your pretender perishes?)
A Chalice can be made, GoH casted, or Faery Queen summoned. But if he's just going to get diseased again, might as well just forge a Ring of Regeneration, and keep the crippled pretender alive indefinitely doing nothing in a safe location.
Sure he'll accumulate more and more afflictions and become more and more useless, but hey, the people needs to know that their God is with them somewhere! Perhaps 50 turns later, you can post in the affliction record thread about a incredibly afflicted pretender, and set the record
Have fun ^_^
-Gateway103