I think in this case the architect should withhold the final payment for the contractor since the contractor did not follow the contract document. Revise the contract documents and try to find legal advise, since any inconvenience due to the negligence of the contractor and the owner could bring legal problems to the architect.
The architect can request a written variance from the building department for the code violention, and request the owner to give him a written document that the architect has no further responsibility for the material being used. And then terminate the architect’s contract with the owner.
Francisco Cuevas Lopez