Yes the cruise control will disable when you pull the clutch.
We are using only engine speed to control speed using the electronic cruise control. The unit has a built in function to disable when it sees a sudden increase in engine speed. When you pull in the clutch with the cruise enabled, you will get a quick blip of the throttle.
I normally disable mine by tapping the brake (if I slow for another vehicle and plan on using the resume function), or will just turn it off completely. The only time I've used the clutch to shut it off was during testing, and if bad things happen.