Sometimes when I work on Thinkpads/MSI laptops, the Ctrl and Fn key are swapped (Fn being the leftmost key), and it drives me nuts - I keep
Sorry. As you mentioned, the Fn key isn't processed by the OS, but received as tuples of Fn + [key] . The best you could probably do would be mapping every Fn + [key] combination to ctrl (and that's only if you never use Fn keys).
Edit: Found this. Before you give up hope, might want to give it a try.
As stated above the Fn key generally operates on a lower level than the OS and hence modifying its behaviour Generally this depends on the manufacturer. Some manufacturers who are not jerks generally provide an option (typically in BIOS) which will allow swapping Fn - Ctrl keys. I have also heard of people taking the extreme option of physically modifying their keyboards (opening them up and rerouting the circuits in the wafer) to swap the Fn - Ctrl keys.
Thinkpad specific: Lenovo included a bios option for their Tx10 (or Tx20? not sure) and above series laptops for Fn - Ctrl switch.
For older models, a user called middleton on forums.notebookreview.com has posted a series of modified BIOS's for lenovo laptops that swap the Fn - Ctrl. It should go without mentioning that as these are completely off-reservation they are to be used at ones own risk.
http://forum.notebookreview.com/lenovo-ibm/474396-fn-ctrl-swap-all-lenovo-laptops-solved.html
If I ever make a lot of money I will contract out hitmen to track down and execute those responsible for going against such well established standards.
On my HP laptop, for whatever reason, the designers decided to put a column of the quick-function media keys. So, at the bottom most-left corner of my keyboard is a calculator key, rather than the Ctrl key.
I found a piece of software called KeyTweak that I use to remap the calculator key to the Ctrl key.