Agreed- they would have to prove that someone at Boeing knew the system was flawed, and pushed it through anyway. I don't believe that's the case, no matter that the NYT, CNN, etc. might say about it.
From what I know the FAA certification process isn't that much different than other first-world country certification processes, I would be surprised if the Euros and FAA didn't rely just as much on Airbus for certification as they do Boeing.