We saw the end of the dreaded Space Herpe durring the last battle, as the ship went through the Time Warp. This is true. But, we also saw the deaths of Nanny and Killjoy. Once out of the Time Warp, when everyone had regressed back to their age upon entering, Nanny and Killjoy were alive and well. There is no reason to think that the Space Herpe didn't regress back to its living state as well.