What I would try:
Open the keyboard settings pane.
Go to application shortcuts.
Select "all apps".
Would it be possible to assign "control-click" to do something else?
Having said that...
... I have to ask:
WHY do you want to disable the standard "control-click" to something else?
If you're using a Mac laptop, seems to me you can just go to the "trackpad" pane and disable "control-click" ...?