You don't have to detect when it's active; you can just always disable it -- well that is, you first have to check if your GCC version supports it at all, it will bail on the command line flag otherwise.
Thats what I meant. You have to know when to use the disable flag.
So you should just try it out somewhere in your build system -- gcc -fno-stack-protector -S -xc - < /dev/null -o /dev/null or something similar, grab the return code -- and that's all you need to do.
Maybe FC6 and/or Ubuntu will change their bad bad ways, but there are so many of those systems out in the field already, lots of projects have to protect themselves against this crap now. Sigh.
Segher