I have the same concern that you do...and really the only solution that I know of is really a pain in the ass. but it works.
What you have to do is boot up into OS X, then open smcFancontrol (I'm assuming you already have it). You change the RPM to whatever you want, I usually just switch it to High RPM. Then you have to *RESTART* the computer and boot into Windows. By restarting the computer you have left the fans running at the speed that it was already on. So essentially, you are just turning on the fans and leaving them on. It's not a convenient way, and you don't really have control over the fans once you boot into Windows, but it works.
I started off running Crysis in XP, and it was extremely hot. But I could tell a difference once I started using the fans. I'm playing TF2 and games like that now, and it still gets pretty warm, but definitely not hotter than 80 degrees C.
hope this works for you
BTW if anyone knows of a fan controller that works in Windows on a MBP please tell us haha