They are his toys. Change the configs to something you can live with or don't play with his toys.
The very idea that I can't mod a mod is yet another problem I have with the Minecraft community, currently. CovertJaguar is an ideal example.
I'm not trying to be hostile here. You can change a vast majority of his 'balance' options in the config.
Look I don't agree with all the GTs choices. But your mad at something he made that is completely optional to use.
Again, as I've said, his config files are a confusing mess, and I wouldn't be surprised if they're that way intentionally. He has recipe changes in GregTech.cfg instead of one of the TWO recipe.cfg files, for example. Ditto his own recipes. His "documentation" is about as vague as possible.
Essentially, altering his config files is about as non-trivial as it's possible to make it while still pretending to be possible. Considering the way he talks about other people when writing his changelogs, it would not surprise me in the slightest to find out that this is intentional.
Saying "just change the config files" is much easier said than done. To get "storage block" (I never liked that name, but lets run with it) functionality back to standard, for example, it looks like you need to change at least 81 separate lines of text. Miss one, screw one up, and you've got problems. And I don't even know if it's "just" 81 lines. For all I know there are other options buried in his config files that I haven't been able to figure out yet that also effect that section of the game.
Want to restore the tin cell recipe to default? Well, first you have to stumble across the fact that it's probably NOT default by stumbling across it in the config files. (Unless you played IC2 without GregTech before, which I haven't.) Then you have to go research what the 'default' is, rather than just having it there in the config file, which would be an entirely trivial thing to have. Ditto for other settings, like upgrade stack size.
Or you might not stumble across other changes until you and thirty other people have already gone through the work of changing the config files and distributing them to everyone.
Changing the config files is a non-trivial process just by its nature, and his attitude, organizational skills, and lack of documentation make it that much harder.