For languages that can emit clean ESM JavaScript source and don't depend on special tooling or runtime support you can totally drop the generated JS files into a Deno project and import them.

...but you're even _more_ on your own w.r.t. bugs, compatibility issues, and the basic assumption that everything will be running inside Node, and therefore trivially able to access e.g. `npx` or various scripting+automation tools.

Your best bet today is to run Node in your development environment, then use the generated code in a Deno service/CLI wrapper/etc. It's clunky, but you can get there.