I did this exact thing.

I left the "save on exit" on. I just edited the emulation station button map CFG file to remove the "favorites" button ("Y" for me) map. (I think I mapped it to nothing. It's been a while.) I can still go into the metadata in FULL mode and edit favorites (I still have a favorites list), but the favorites button do anything. I have the button available in games, just not ES. Again, I edited the CFG file in terminal with nano...or in PIXEL with text editor.