I can’t see a reasons why you not just put your code from the functions.php into Plugins or Must Use Plugins, it isn’t that hard to do and is, in my mind preferable, to connecting this task somehow to the wp-config.php.
Besides that, if you don’t absolutely have to remove the backend/admin themes functionality itself, just remove, unset and/or make it inaccessible from the backend/admin area. Seems more practical to me, probably not knowing all the determining factors of course.
Edit: this is complementary to what @ravs suggested