I've written batch scripts with WP-CLI and mysql to spin up new sites, from scratch, including database creations, install latest core, a suite of base plugins, install themes and create child themes, and configure some options. Works a treat.
Pantheon (hosting) provides a lot of tools for managing Drupal sites like this. Now that they also support hosting Wordpress sites, they may offer similar tools. Might be worth a look: getpantheon.com
Have you tried WP Multi-Site?
I use wp-cli pretty much every day at work
wp cli is the bomb, try it, it rocks!
EDIT: So it turns out there's a third party project that kinda sorta does this: WP-CLI (http://wp-cli.org/). Anyone used it?