So the other possibility that does not require more developement, and is not hacky:
Create a directory that houses all your source pandoc files. Use a script the processes these files, using pandoc or what ever you want, with an output format of “markdown”, and output into the content directory.
In that way, you are basically using pandoc as a markdown pre-processor to feed files to Hugo. You can pass any options you like to it, apply any pandoc filters you like, and refer to any bib files you like.
Though an improvement to hugo would be preferable, this setup seems like it would work quite well, without aliasing pandoc to a wrapper.