Simple solution: Kill him off, go AI and start a new game in a later age .. at least that's what Sauron did
1 year are 12 turns .. waiting 5 years (60 turns!!) for an affliction to heal does not make sense in Dominions - gameplay-wise, at least. Story-wise it should be millenia (just like in all those stories you mention...), though.
Maybe simply some more pretenders should have recuperation - would be thematically fitting for quite a bunch of them. For others, on the other hand, surely not, e.g. lots of the inanimate ones.
On the other hand, I'm not sure if I like the idea to have even
more SC pretenders in the game :/