MINI Cooper S - Noisy Cooper S

Q
Two months ago I took delivery of a brand new Cooper S. I have just had the JCW performance upgrade fitted by the MINI dealership. I enjoy the extra power (though not massively different) but don't like the extra noise. I presume this is from the sports exhaust? If so do you know if refitting the original exhaust, but keeping the other parts of the upgrade (air filter, chip etc) would cause any harm? If it didn't cause a problem, would I still have the performance benefits?

A
Removing the JCW exhaust system and refitting your original system should reduce the performance of your Cooper S, but you have pointed out that the extra power isn't massively different, so you probably won't notice it. However, all of the JCW performance modifications are designed to compliment each other, so we'd expect there should be a reduction of power output and delivery of power as the exhaust system is a major component in this upgrade.
Before deciding to change back to your old exhaust system, have you looked into where the unwanted noise is coming from? It may be panel vibration or sound resonation from the exhaust that's being transmitted through to the interior of the car. If this is the case, you may find some additional soundproofing can reduce the unwanted noise.