Hi,
you can check the cpu load of any program in the task-manager. Freetrack is using probably around 3-4%. Freetrack does not use gpu calculation.
My question then is: could in any way the use of freetrack harm my gpu?
No, there's no way to kill a gpu with Freetrack.
Try to file down the LEDs to get a better beam angle could be a solution for your tracking problems. A nailfile and some fine sandpaper does the trick.