I have also found that sometimes providing the client with a firm NO is not as scary as it seems. What is the worst thing that can happen? Ya get fired, but most will respect being told NO if you have a valid reason. One needs to remember as a design professional or contractor buildings projects are a daily activity. On the other hand unless the owner is a developer, they have typically only do one or two building projects in their entire career. Many owners are relying on your expertise and judgment as it relates to a building project.
I have been in a unique position over past several years doing investigations into building failures. Most times I have access to the project files which provides 20/20 hindsight. You might say it is easy to sit on the sidelines and critique a building project, actually sometimes it is painful. You can pinpoint the moment the train came off the track so to speak. Too often no one wants to say no because NO in construction language means STOP. However most times it could be as simple as answering a few questions that would have revealed larger problems later in the project.