I may have solved this problem the hard way, but I created a script using a scripting program (glovepie) along with a joystick emulator (PPJoy) to create a virtual joystick with the proper axes that's controlled by the physical one. I put enough effort into it that I figure it's worth posting for others to enjoy as well.
You'll need glovepie, which can be found here, and PPJoy which can be found here. The glovepie script can be downloaded here. Instructions for setting up the virtual joystick are in the script comments.
I didn't mess with the hat switches, the scroll wheel, selector, or any axes other than pitch, roll, yaw, and thrust. If that's a problem, it shouldn't be too hard to look at the code and figure out how to work them in yourself
This could also be edited very easily to fix problems with other joysticks, and will work with any game that uses a joystick.
If ya have any questions, feel free to ask.