There's a switch on the clutch pedal (it's like the brake switch) , which senses (and is read by the ecu) when the pedal is depressed. So, it's quite possible that the ECU doesn't see the pedal movement, and therefore does not tweak the revs to compensate. Check the clutch switch is actually moving when the pedal is depressed. Removing the switch, and fully extending the plunger might help, but a replacement would be best, as it will self adjust when installed. A scan would probably show clutch switch fault code, or what ever else may be the cause of your rev fluctuations.
Is this the same car as had mysterious symptoms a while back?
Mac.