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While I would not want to allow my Cthulhu to be killable, per se, I would want it to be defeat able. There was one story by Lovecraft in which Cthulhu (IIRC) is chasing a man upon a boat. The man runs for his life but in a last ditch effort, turns his ship (something large) around, and straight up rams the elder terror. It falls into masses of goop and actually begins to reform, but the man escapes before any more terror can find him.
My short, comical explanation aside, Cthulhu is nigh indestructible. However, I see enough damage could be done to turn it back. Make it sleep once more in its city of R'lyeh.