You should take the contract between you and your architect to an attorney for analysis. The terms of the contract will govern concerning what your architect is or is not responsible for. If the contract clearly put the burden on your architect to perform in a certain manner and he failed to and there are not additional clauses that reduce his liability, then you may have a claim. If you have a claim you will need an attorney to pursue that for you, so you may as well hire one now to help you determine if you have a breach of contract case or not.
This may not be an issue just involving your architect. Malibu is notoriously anti-individual property rights. They deny permits on a whim, and it would not be surprising to me at all that they changed the zoning because of the nature of your project.
You need to find an attorney with experience in real estate and zoning issues, and best if you found one who has dealt with the City of Malibu before. You may have a very expensive lawsuit on your hands, and it might not be your architect that is at fault.