The worst part about Git is the bad defaults. Seconded only by mismanaged storage. Or maybe being designed for the use-case most of its users will never have. Or maybe horrible authentication mechanism. Or maybe the lack of bug-tracker or any sensible feedback from its developers.
None of this can be helped by the GUI. In fact, beside Magit, any sort of front-end to Git I've seen is hands down awful and teaches to do the wrong thing, and is usually very difficult to use efficiently, and mystifies how things actually work. But, even with Magit, I'd still advise to get familiar with CLI and configuration files prior to using it: it would make it easier to understand what operations is it trying to improve.