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I've found a possible way of doing what you have described:

http://live.gnome.org/NetworkManager/Debugging

Have a look about half way down the page at the bit that looks at...

Just so you don't feel too alone, I'm looking for the same answer. I have a different issue, but it boils down to being able to pass the ap_scan=2 mode to wpa_supplicant using network manager. ...