I am having CPU spikes as well.
I am running Mainstage 2.2.1 on Lion, on a new Mac Mini Server, i7 with 2 SSD and 16 Gigs of RAM. The spikes, as far as I can tell, are specific to Kontakt 4, and more specifically related to use of the sustain pedal. Even in an otherwise empty concert, running Galaxy Vintage D piano in Kontakt, where the CPU usage is around 20%, occasionally when lifting the sustain pedal, or less frequently while depressing it while playing, the CPU will peg, and I will get pops.
This does NOT happen if I run Kontakt as a standalone app. It is absolutely specific to Mainstage. Even running Galaxy with all its functions (harmonics, pedal noise, etc) turned off, the problem still occurs.
I do not get this using the same controller (VAX77) with Ivory, or with any software pianos (I own a few from Sampletekk) loaded into EXS24. Those same pianos loaded into Kontakt will glitch on me.
So Native Instruments might claim that it is not on their end, since standalone Kontakt works fine. And Apple may claim that it is not on their end, since other instruments work fine. All I know is that Kontakt does not work glitch free at all for me when playing piano and using the sustain pedal within Mainstage. I am going to try to figure out how to run standalone Kontakt as an external instrument and see if that kludges a fix for me, as this functionality is quite important to what I do.