Okay finally here's how to remove all those "phantom" bound keys that you can't unbind within BF2.

Go to
My Documents\Battlefield 2 Demo\Profiles

Open up Global.con

Note which profile it's using (I Default, 0001 and 0002 and mine was set to 0002)

Open up Controls.con

If you look at the top line for each subsection, it says Infantry, Land, Air, Helicopter, Sea, and Default. Each is pretty self explanatory with the exception of Default. I believe this is what ingame calls "Common".

The bound key is at the end of the line

IDKey_Key Name Here

Delete the whole line of the occupied keys you want to change. OR Change it to an unused key of your choice. Some of them were probably taken out last minute (like Left Alt was set to Toggle 3D Map but there is no way to change that ingame. and X is set for Flare in Sea. Can you even fire a flare in a boat? I never tried.)

Save the file.

Now you can bind them ingame.

Enjoy.