I'm surprised ASUS is giving you problems with your chipset fan. About 7 months ago the chipset fan was dying on my sli deluxe board so I called those people at ASUS support. I was on the phone for maybe 5 mins with them and they said they would send me a replacement as soon as the new shipment of fans got in. This was a monday that I called and sure enough the following saturday I got a package in the mail from ASUS, the new fan. It has been running like a champ ever since.
As far as replacing the fan it didn't bother me too much taking out the motherboard because I had to swap power supplies anyway. Although I did slice my finger somehow

and got blood on the mobo...ouch. Whichever way to decide to fix your fan issue, watch out the computer doesn't bite your finger!