Its debatable if the fans are really even necessary. I think its there for peace of mind. If you've ever removed the northbridge hsf you'd see that its usually not even making solid contact with the northbridge and sometimes doesn't even have any thermal compound. I always have to lap it for about 25 mins for it to even be flat, and the AS2 I applied the first time made an imprint on about 1/4 of the heat sink the first time around. If you disable the fan, worst thing that will happen is that your system will become unstable and you'll probably get some BSODs. Disable it, if it runs fine, then you're in the clear. If you start locking up, then plug it back in. Unlike your CPU, your northbridge isn't gonna fry w/out a fan.
Chiz