There're a lot of places where you can set/change these keybindings:
- System Settings / Keyboard / Shortcuts / Launchers
- CompizConfig Settings Manager / Desktop / Ubuntu Unity Plugin / General
- CompizConfig Settings Manager / General / Gnome Compatibility / General
I did check the first two, but Alt+F1 and Alt+F2 were still grabbed by the system. It took me quite some digging to find that I had to disable this in CCSM's Gnome Compatibility plugin as well.