I'm in agreement with pretty much everybody here. It's worth noting that it is straight up impossible to prevent 100% of the cheating due to the nature of emulation. Anybody could alter the emulator, alter the ROM, or any number of things, so it's never gonna be 100% cheat-proof. That said, I agree that we should do whatever we can to prevent casual cheating, so that at least it's difficult. But again, we're limited as to what MAME allows us to do.
Per the .cfg files, at this point I don't think we can just delete them on startup. However, I will examine the contents of the files to see if there's any way I can modify them to remove only certain customizations, to see if that helps things.