It seems the mapping is local to a buffer as it was defined with the argument <buffer>.
When you type :unmap y<C-G>, you ask Vim to unmap a global mapping whose {lhs} is y<C-G>, but there's probably no such global mapping on your system hence the error.
If you want to unmap the local mapping, you have to use the same argument <buffer> which was used to define it: :unmap <buffer> y<C-G>
Edit:
To automate the process you could install an autocmd watching the events VimEnter, BufNewFile and BufReadPost. It would test if the mapping exists if !empty(maparg('y<C-G>', 'n')), before trying to delete it. It could give something like:
augroup custom_fugitive
autocmd!
autocmd VimEnter,BufNewFile,BufReadPost * if !empty(maparg('y<C-G>', 'n')) | unmap <buffer> y<C-G>| endif
augroup END
You couldn't write this in your vimrc because the latter is sourced before your plugins which would override anything you do. Instead you would have to write it inside ~/.vim/after/plugin/mappings.vim. The filename (mappings.vim) doesn't matter, only the directory is important (~/.vim/after/plugin/).
Edit 2:
As your last comment says it, it seems there's another way to disable the mapping. fugitive install the mappings <C-R><C-G> and y<C-G> only if g:fugitive_no_maps is different than zero. So if you include let g:fugitive_no_maps=1 inside your vimrc, y<C-G> should not be defined.
fugitiveplugin. – Alexey Apr 09 '16 at 21:13