If your compiler does not support long long, there are a whole bunch of
*other* parts of the C standard that it does not satisfy, and you will
probably find that you will fight other unnecessary battles.
One possibility would be to compile CLANG+LLVM for your target. If that
is not possible, perhaps GCC?
The C backend generates long long for 64-bit integer types. If you're C compiler doesn't support a 64-bit integer type, you'll have problems. If it does, but spells it differently, you could hack the CBE to produce the right name.
Is that true for the freestanding header files? We have not found it so
in the C backend for BitC, though admittedly it was a design objective
to avoid exactly these conflicts. I would think, in particular, that
stdint.h and inttypes.h would both be safe.