Actually when you blew up that stupid crystal in the mission, you were technically banishing his soul to a nether realm. So the first part of CE is running through the meat grinder with all those thrall and that big white light you run into at the end is a portal to Crota's nether realm. Once you kill Crota in the nether realm, you supposedly destroy him forever.
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Yes, that really worked well...Not. I can still return to the Hellmouth and slaughter him over and over again.
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If you wanted continuity, the first time you were killed in a darkness zone you'd be done and your character would automatically be deleted.
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Well wouldn't that be nice, a game with actual challenge...