I looked in the option metadata for our C/C++ frontends and -Wduplicated-branches isn't flagged as RejectNegative, so -Wno-duplicated-branches ought to work; I think you ought to be able to set that on a pragma. Does that help?
I understand why this is true and very hard to fix (thus I wouldn't even mention it except you were asking about UI issues rather than code generation issues). But it would be user friendly if GCC could warn of this rather than silently ignoring the flag when using the #pragma...ignored/#pragma...pop model.
By the way there are many such flags that cannot be used in a #pragma...ignored, I just glanced at our source code and grabbed one example at random.