My old Toshiba (2 machines ago) made the exact same sound when it throttled the CPU...of course it was a piece of crap too...
The sound doesn't really bother me...and if it does (when plugged in), I just use the MagicNoiseKiller thing....
As people have noticed on the apple message boards, there are no power management drivers on the MBP, so it is relying on the chip to do everything. If they were to write drivers to use the built in speedstep functions instead of what is currently used (sleep commands), the sound would likely go away, and we'd see an improvement in battery life. Let's hope Apple does this (and the "diagnosis" is correct).
Either way, I still think it's a great machine.