Configure Modules from a Script

Question

I'm interested in created a sort of "deploy" script. I basically want it to take a fresh drupal install (plus my versioned work in sites/) and disable and enable modules as needed and then automatically configure the site.

The first part is easy with a simple script and drush. The second part is the part I'm not so sure of. I can manipulate the database directly (again, using drush) and run queries against it, but I wonder if that is a bad way to do it since the schema of modules can change when they are updated (though I think core will stay mostly the same in 7.x).

I'd like to be able to script things like the CSS/JS aggregation settings or the Facebook APP ID/Secret in fboauth. Is there any "safe" way to do this without worrying about module updates breaking the script?