
the key problem with clamping carbon bars into a stem is that any burs (poor quality finish etc..) can cause deformation of the bars which cause stress risers and therefore weaken the bars.... (as Matthew said)
so as long as it's a quality stem you should be fine....
personally I use a RF Deus with a RF Air Alloy XC as Im a tad on the punishing side with my bike and dont fancy snapping carbon bars (mainly cause I cant justify the cost of the Monkeylites....)
you'll obviuosly not want to scratch the bars when fitting the shifters brake levers etc...