Auto sound levels will vastly amplify the sound on the recording in a quiet environment, but in reality you should barely hear the iris operate.
Agreed that a clip will help. I suspect it is the aperature changing. As Paul states, that is the only mechanical action left. I disagree that you would barely hear the iris operate. I certainly have some lenses where this could be characterized as a grinding sound. My Zeiss 85mm is quite loud when changing aperature. Indeed, it makes a grinding sound. But, I never use auto exposure while shooting video (and don't recommend using auto exposure for video). If this is the grinding sound, then you'll easily get rid of it by using manual exposure.
And, yes. You can set the 600D/T3i's audio manually without Magic Lantern.