Session Data vs. Config Variables

How would you implement option 2 - overwrite config.php file?

Fairly easy. In autoload.php I added this:

$autoload['config'] = array('sub_navigation_entries');

and placed sub_navigation_entries.php in the config folder. This contains just the arrays with the specific values.

Only thing left for me to do is to create a cronjob shedule the recreation of the file maybe every 3 hours or so. In case someone hits the a view while the file is written I have added a fallback to caching & database query into the menu-code.