You define a package for your own project that depends on libsodium/zeromq/etc from GuixSD. Then you export your own package with 'guix pack'. For an example of what a package definition looks like, take a look in /gnu/packages in the GuixSD repository, for instance libsodium [1] or Vim [2].
I did something similar recently to build an Nginx "application bundle" [3]. It uses Nix (previously Guix, but Nix worked better for me in the end) to build a squashfs image. You can then run the binary on that filesystem with systemd-nspawn, or as a regular service by setting RootImage=. Some advantages over the Docker approach are that you can easily customise the build (e.g. changing the ./configure flags for Nginx without having to manually perform all other build steps), and bit by bit reproducibility (if you build the same commit six months from now, on a different machine, you will still get the same image out).
[1]: https://git.savannah.gnu.org/cgit/guix.git/tree/gnu/packages... [2]: https://git.savannah.gnu.org/cgit/guix.git/tree/gnu/packages... [3]: https://github.com/ruuda/miniserver#readme