If it's "clicking" when zoomed, it probably has nothing to do with the aperture.
You can't change the aperture with the lens off the camera, anyway. The only way to test the aperture is by setting it to something smaller than the max (f2.8 in this case), and using the depth of field preview button on the camera to stop the lens down. If you remove the lens while holding the DOF button, it will remain stopped down.
However, I doubt that messing with the aperture will effect the clicking noise one way or another. The aperture and zoom mechanisms are two separate things. More likely, there is grit or something loose in the zoom mechanism. I'd send it to Canon to be checked. Or, if it's no longer in warranty, take it to a local camera repair tech, if you can find a good one.