As vfb wrote, you've got a pretty good handle on how afflictions work. AFAICT, afflictions were designed for precisely the purpose that we find so annoying. In other words, afflictions are a counter to having one uber-unit that smashes the entire map. You can still build the uber-unit if you really want to do so, but afflictions will limit its usefulness sooner or later.
You did forget one method of healing afflictions: Faery Queen. She's a non-unique Nature summon, so any nation with decent Nature magic can get a few of them. If you don't have decent Nature magic on your national mages ... um ... hope for good luck with an independent mage?
Also, someone once made a mod that gave all Pretenders the "Recuperation" advantage. If you use that mod, you can at least have an un-afflicted demigod....