There is a way to do this. On a 64 bit machine running .NET 4+ the GAC is actually here: c:\windows\Microsoft.NET\assembly The path you're referring to is for 32 bit apps.
Try searching for your registered DLL in that folder and place your config in the same folder.
However, placing configs for a DLL in the GAC is not a good approach according to this: http://stackoverflow.com/questions/311253/config-files-for-assemblies-in-gachttps://stackoverflow.com/questions/311253/config-files-for-assemblies-in-gac. The config should technically be part of the app that uses the DLL and would go in its BIN folder.