You can 'Configure' the 'Slots' for the Folding@Home software using the F@H 'Advanced Control'. If you have a GPU, then you can remove the CPU Folding Slot, and the FahCore_a4 process will not run (it is only used to do CPU folding).

If CPU folding is your only option and you still want to contribute, where the F@H software was slowing your computer down too much: you can change the F@H settings to 'Medium' or 'Light', or 'On Idle'. There is also a Chrome plugin for Folding@Home for CPU folding that is better for laptops and less powerful computers without a GPU.