This cannot work reliably and automatically at the same time. Remember that GUIDE cannot know, if a callback is used from anywhere else in the code. While a direct call could be identified automatically, you could hide it in feval or eval. Therefore I assume, that you have to remove the code manually.
I'm using GUIDE to design my GUIs. But as soon, as the layout is ready, I convert the figure to code. See e.g. https://www.mathworks.com/matlabcentral/fileexchange/20152-guidegetter.
