StarCraft 2 doesn't have a frame rate cap by default and if you'd like to have quieter fans while playing it, it would be better to put one.
For example, if at your current settings, your CPU/GPU are capable of pushing out 100FPS, they will, but it's useless since most people aren't able to tell the difference when it's over 60FPS (for some it's lower). You'd be better off imposing a 60FPS limit so that your CPU/GPU aren't always at full load.
You can also set a separate FPS cap for the menus. Even while in the menu, StarCraft 2 generates the background 3D graphics at maximum frame rate so your computer can't even take a brake to cool off in between games.
All you have to do is modify a text file located at ~/Library/Application Support/Blizzard/StarCraft II/Variables.txt
~ is your username and make sure Library is visible because by default it's hidden in Lion.
Open Variables.txt with TextEdit and add those two lines anywhere in the list of variables:
frameratecap=50
frameratecapGlue=30
"frameratecap" represents your maximum frame rate in game and "frameratecapGlue" represents the maximum frame rate of background 3D elements (planets and stuff) in menus. Change the numbers with your desired max frame rates.
Supposing your MBP was pushing higher frame rates (either temporarily or always)than what you set it there, you fans should be quieter since your CPU/GPU won't be working at full load 100% of the time, which obviously forces the fan to always be at full speed.
EDIT: Before putting a frame rate cap, it might be a good thing to know your current frame rate without the cap. Press Control+Option+F while you're in StarCraft 2 to display it. To get best results, make sure your current average FPS is significantly higher than the FPS cap you will put. For example, if you were to put a 50 FPS cap, adjust your graphics settings so that you get 70-80FPS before putting the cap.