Yes, I run one with the latest FSO builds. You'll see that on the FSO release posts that there are two .dlls that you need to download if you want to use TrackIR. Apart from that extra five seconds of work, it works well and it's very easy to use.
Only other things that I'd recommend would be investing in the TrackClip Pro so that you don't need to wear a baseball cap every time you want to play Freespace. This assumes you wear headphones, otherwise maybe go for the baseball cap option. I don't know if you use a joystick/HOTAS in Freespace, but mapping the reset button (as moving your chair etc will throw off the "zero") to convenient button will help as well.