No, but not because the CoC defeated him. The CoC just beat the avatar of Jyggalag, which would not prevent the Prince himself from doing, well...anything.
However, there's no reason that Jyggalag will not return to the Sheogorath-cage that he was in before, in time. The Daedric Princes can just curse him again, and the whole situation has happened before. Arden Sul stopped the Greymarch and became Sheogorath just as the player did, and he ended up becoming Jyggalag too. I assume that once Skyrim happens, Sheogorath will be back to his old self and Jyggalag will be trapped inside the madness again.
I was under the impression that the CoC was the first to actually defeat Jyggalag before he could conquer Sheogorath's Realm, whereas Arden Sul and the other Champions of Sheogorath either were killed or fled the Shivering Isles. Jyggalag himself says that the CoC released Jyggalag from his curse, allowing him to remain in his true form.
As for Arden Sul stopping the Greymarch, remember that the priests of the Sacellum Arden-Sul both tell you that he died.