I had an identical issue on a 2009 Clubman that started from the time I bought the car. I documented my experience in a thread on here. Was a knocking noise at idle that disappeared when the clutch pedal was depressed. I informed the dealer about it during the warranty period. Sometime after 55,000km, the clutch failed. Because of my initial complaint BMW/Mini covered part of the cost. It was, nevertheless, still not cheap.
That having been said, I am now on the second clutch which has been in the car for almost 70,000km and I can tell you that there is a similar - but slightly different - noise. Small rattle at idle rather than a knocking. With the clutch in the noise goes away. The clutch seems to be fine and I agree with the previous poster that this is normal transmission noise.
In any case, I would just drive it until it fails and stop worrying about it. If the clutch isn't slipping you shouldn't worry about it. All clutches need to be replaced eventually anyways.