I don't know if GPU3 supports this yet, but the ATI GPU2 folding clients do allow you to set how much GPU usage you want in the same way uniprocessor clients allow you to set CPU usage. This way I have my Radeon 4870 using 75% of the GPU for slightly reduced temps (the card isn't a marvel of efficiency

)
The option is:
CPU usage requested (5-100) [100]? for the console version when you do a -config
A slider bar for the systray version
You could give that a shot, or try undervolting + underclocking the cards if your software supports setting custom clock / voltage when a program is run.