src: make `FreeEnvironment()` perform all necessary cleanup

Make the calls `stop_sub_worker_contexts()`, `RunCleanup()`
part of the public API for easier embedding.

(Note that calling `RunAtExit()` is idempotent because the
at-exit callback queue is cleared after each call.)

PR-URL: https://github.com/nodejs/node/pull/30467


Reviewed-By: James M Snell <jasnell@gmail.com>
Reviewed-By: Gireesh Punathil <gpunathi@in.ibm.com>