You could always run it through steam big picture mode, then you can rebind to your heart's content!
How do you do that? I don't play with steam
You can add gta-sa.exe as a non-steam game in your steam library. There is a button to "add a game" on the bottom left of your library page.
Then, start big picture mode (there is a tiny icon on the top right that looks like a controller) and browse to gta-sa in your library.
You can access the controller options there. What controller are you using? Steam supports the Xbox, PS3 and steam controllers.