Can't we just count ##### as a 'legitimate comment' so it doesn't break existing map shaders (which worked previously because of the vanilla bug)? And then make it warn about 'out of date syntax', but accept it anyway? Obviously incomplete/not very thorough at all but something like:
if(token[0] == '#' && token[1] == '#')
{
ri->Printf(PRINT_WARNING, "WARNING: Shader File %s contains out of date syntax, that does not comply with existing shader standards. ## is not an acceptable form of comment, please use c style comments.", filename);
break;
}