I dont know if this still works after the update, and its certainly not a solution (since it removes the point of having a dual core laptop) but I would be shocked if apple didnt accept this as proof of the cause of the whine:
On the install discs, on disc one, there are a load of tools (developer tools or something). One of the packages (CHUD package) installs a small tool which gives you processor settings in the menu bar and in system preferences.
Using this you can select 1 or 2 cores. If you select 1 core, the mbp turns near silent (i.e. whine gone) which to me proves undoubtedly that the whine is due to powersaving on the 2nd core.
Whilst this does remove the point of being dual core, it sure as hell saves battery life, and my temperature drops by about 5degreesC according to my temperature widget (it feels a lot cooler too).
Anyway, it could be worth seeing if this still "solves" the whine after the update.