This all sounds quite weird.
darktable is build against libgphoto2 (required version >= 2.5), mine is build with 2.5.27 for example. I assume your darktable is started from a user account (not root). How should darktable damage this library (usually in /usr/lib/x86_64-linux-gnu/libgphoto2/ (root !) at runtime?
To my understanding gphoto2 (the command line client for libgphoto2) is not used by darktable at all. I have not installed it in my system at all.
In my system I cannot find any configuration that could be assigned to libgphoto2.