This is probably a dumb question, but I'm gonna ask anyways: how much torque/horsepower can the stock rear end take? And what component is most likely to fail first?
I believe that Ford claims the 8.8 to be something like 10% weaker than the 9". I don't buy that claim myself.
More importent than how much it can take is how it's used. Vehicle weight, gear ratio, power, slick/radial/drag radial, manual or auto, all play a part.
As for what will fail first? My first concern would be the axles. GT axles are exactly the same as the V6 axles.
If you're going to seriously drag race with slicks, skip the 8.8 and swap in a 9". It's stronger, has greater aftermarket support and it'll get you the captured axles that the NHRA/IHRA require at certain speeds.