As I understand you need to use windows tools to flash the BIOS. In windows you can also set the fan speed with in an xml config file, but I don't see that there is any program nor driver for this in Linux. So best solution is to get the card flashed with recommended fan settings.
After beeing annoyed for a while because of changing fan speeds on my HD4870, I've modified the video bios to allow quieter operation.
My card is a MSI R4870-T2D512-OC, originally at 780/1000MHz.
The Windows tools I used was:
GPU-Z, for extracting the bios from the card)
(ATI)WinFlash, for flashing.
Radeon Bios Editor (RBE), for changing the frequency and fan controls in the BIOS files.
The things I changed was frequencies down to 750/900MHz, lowered voltages when in powersaving modes, increased voltages when in performance modes (card was unstable at stock voltage and memory speed of 1000MHz, the cards were later altered to ship at 780/900MHz), altered fan to kick in a bit higher (40C/106C), enabled PWM and set hysteresis to 10%.
All this made the card a bit cooler, and the fan finally runs stable on low speed while in powersave (2D) mode.