Well, contrary to what many insiders claimed, Kahn did not survive his encounter with the Deadly Alliance. He's still quite dead(And apparently no one even bothered to move his corpse from the place it was slain). However Spoiler......
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In Havik's ending he consumes the heart of Onaga, absorbing his ability to raise the dead and resurrects Kahn! It appears reviving Kahn is his plan to ensure choas continues to dominate the realms!
Though I doubt the heart consuming part will be cannon, this still brings hope to Kahn fans that the emperor will be present in a future MK title, as Havik's mission seems seems to be ensuring the chaotic emperor's return.