For an example, given the following:
5D M2
Gitzo tripod with weight
Mirror lockup
cable release
For a variety of shooting condtions with Canon IS lenses, under what circumstances will IS be a disadvantage, if any?
Depends on the lens. For very long lenses like the 500 f:4, IS is a godsend at any time, and greatly improves sharpness even on a tripod. For the elderly 100-400 zoom, you must turn IS off when it's tripod mounted because it gets confused and dances around. For a short lens like the 24-105 f:4 L, planting your rig on a solid tripod will gain you far more sharpness than IS ever will. I turn it off with this lens unless I'm hand-holding the camera.
Finally, I haven't really seen any advantage to using IS with the 70-200 f:2.8 when it's tripod mounted, unless I have the head loose and I'm tracking a moving subject, which is a pretty rare event.