I seem to be having the same problem on 11" with i7.
The CPU load is 2%-5%, but the CPU temp is 80° C. Fan is constantly on when connected to thunderbolt.
I especially noticed this last night when I lay in bed (not connected to thunderbird), watching YouTube clips, and the fan wasn't noticeable at all. I can't be sure that it's due to the thunderbolt display, but I've been having this issue ever since I replaced my 27" Cinema Display with the 27" Thunderbolt display.
I have MBA 13"/ i7 have exact same issue. If I reset the SMC the problem goes away. However I have to do this everytime i dock / undock from the thunderbolt display. Very annoying!