Fatal error: Call to undefined function _system_default_theme_features after rebuild, followed by non-recoverable(?) errors

After doing a git pull, I am often presented with an error about rebuilding, that contains a link to this page: https://drupal.org/documentation/rebuild

As a good citizen, I follow the instructions and replace my settings file and delete my files/php directory (even though drupal was previously installed and working fine, complete with data in the database).

But after following the steps above, I'm presented with a fatal:

I believe this is because my config directory hash has been regenerated, so the previous theme settings that were saved in the previous config directory are now lost.

Since I assumed this was the case, I deleted my config directories (I now have two) hoping that would clean up the problem, but instead I'm greeted with an even worse error:

When I encounter this problem my general course of action is to drop the database and start over. Is there any way to recover from this situation? and if not, are we already working on makeing Drupal 8 less brittle? Dropping the db and starting over won't be a viable solution for websites when they are actually running Drupal 8. It's making me nervous.

Thoughts about possible solutions:
- if a cached copy of a function can't be found, use a non-cached copy, or rebuild the cache
- automatically generate a new config directory with the correct hash if it doesn't exist (maybe we are doing this already?)
- fall back to the config that shipped with the module/theme/whatever if a site specific override is not found (but log an error)

Possibly related

#1712250: Convert theme settings to configuration system