Oops, I just read "[My main goal is to be able to use Node.js libraries from Rust]". That probably won't work, then . I don't think that Deno is compatible with node modules.
Node.js itself isn't designed to be embeddable, AFAIK. It assumes it exists in a specified location on disk, where it can put global node_modules and include dirs for gyp-based modules.
Even if you embed node executable into your Rust executable, you will still need to have the rest of node's installation on disk.
You may as well just bundle the whole Node tarball with your project. Just launch node executable from disk. You'll get process isolation as a bonus