This is just Italian organising skills in action rather than cycling being amateurish, there's always something that doesn't work and has to be changed at the last minute (the main feature of the stage being removed two weeks before the show at Eurovision last year comes to mind). In any case, provided there's a replacement stage, I would be overjoyed if the MTT is scrapped, whether it's an easier TT (for example up the easy side of Sella Nevea like
@Mayomaniac has suggested previously) or a more mid-mountainy stage (the easiest option would be multiple loops over Cereschiatis and the hard side of Sella Nevea) that replaces it.