I've got exactly the same problem with my Macbook Air 2011 in Windows 7 (Bootcamp), I also would like to swap the "function" key with the "control" key (on the left side of the MBA keyboard).
It should be easy enough for Apple to add/fix this in an update for bootcamp.
A lot of "switchers" like myself have engrained habits from PC (with Control being in the left corner), not least in CAD where Ctrl is used a lot.
It would be nice and appropriate of Apple to address this issue, since they are usually very focused on user experience/ergonomics and customizability...
I've switched some other keys with Autohotkey (such as swapping alt and windows keys, making F12 the print-screen button and so on), which is easy enough, but, in order to change the fn key one would have to mess more deeply with the registry and that doesn't seem very safe or easy for the average user.
It would be highly appreciated if apple could build us a complete key-remapping app for Windows and include it as a download in updates for BootCamp.
It would help a lot of PC users feel more comfortable with switching to mac (likely still using windows for this-or-that specialized need, as do I).
Since they will be able to work in the same way on their ie MBA in "pc-mode" as they did on their previous PC hardware (ie an Engineer who works in the same 3D software for years, on PC, doesnt want to change A THING, which is fair enough), they will feel much more comfortable with getting cozy with OSX...
Looking forward to the good news asap!
Otherwise insanely happy with my machine, fantastic piece of equipment, does everything I need it to (except above).
Cheers,
Lorenzo