As GnuCOBOL knows best how to call the underlying C compiler (depending on the C compiler it was built with/configured for and depending on the given command line options to the GnuCOBOL compiler `cobc`) - I guess this is what is done for Fortran, too - I'd suggest to not use it as a pre-compiler step but as a "real" compiler.
A different thing is that COBOL is often used via pre-parsers (for example `EXEC SQL` and lot of COBOL-shop-specific-self-written-pre-parsers), therefore it would be nice to end with an option for the chain Source -> Pre-Parser-Step X (for example a shop specifc one) -> maybe Pre-Parser-Step Y (for example the SQL preparser `dbpre`, Oracle's `procob` or whatever) -> plain COBOL source -> `cobc` (+ internal: `gcc`, `clang` or `cl.exe`).
And yes, I think a full-integrated approach - which seems to need a plugin, given the comments so far - would be best.