Using S3 for the uploads solves our problems without needing EFS, as we disable file system changes through other methods. Plugin installs or upgrades are great, but aren't tracked in the git repo, so we do those via local upgrades and deploy out to AWS instead.
The article also mentions installing WordPress as being a pain, but you can easily automate this using wp-cli [3] if you want to. Your RDS containing the WP data is going to be shared though, so there's no real need to install more than once.
[1]: https://github.com/humanmade/aws-ses-wp-mail [2]: https://github.com/humanmade/node-tachyon [3]: http://wp-cli.org/