I've added custom temperature control to the avalon code in the cgminer git master.

It now acts like a simple PID controller trying to maintain a target temperature, which by default is set to 45 degrees, so it will try to keep the temp 43~45, but never going below a minimum fanspeed of 20% as a safety precaution and to maintain airflow.

You can modify this value with the new command:

--avalon-temp

Setting this to something very low will have the same effect as turning the fans up to maximum and vice versa.

If you are not running it from a command line, it can be added to the "More options" box in the web interface (once you have the binary on your machine).