At the very end Destiny screamed about Time and Space and a Ghost. I don’t think they really solved the problem at all.
When Morgan Le Fay was held captive in Avalon, Clan Akabba resurrected her. Are we sure Selene didn’t make some sort of deal with the for the same?
While I agree, she appeared to be degraded, Destiny screaming about a ghost suggests it’s nowhere near over. Magic is nowhere near that easily undone. They couldn’t even resurrect depowered mutants until Apocalysw became involved, and he knows magic.
Apocalypse has let himself get killed too, when it suits his schemes.