Perhaps a uBasic command could be added to CHDK to allow control of ISO during video recording?
Ewavr mentions the below commands are available for developers, unfortunately I'm not one but I could handle knocking up a ubasic script.
"Another functions (derived from SetAE_CdsGainValue, can be found on strings "SetCDSGainApex" and "SetPgaGain") allow change ISO during video recording. Of course, AE must be turned off before call it (ExpCtrlTool_StopContiAE)"