Off the bat, I want to mention that I am more of a movie purist, and think the EU is full of factually inaccurate garbage. As far as I know, it is only the EU that tells us that ion cannons are used primarily to disable ships without damaging them. I'm not convinced.
For one thing, the only time we see an ion cannon used in the movies is at the battle of Hoth. The cannon hits an ISD with at least 2 shots. We then see huge flashes of light and color and then the ship turns away while covered with electricity arcs.
Kind of like what happens when a TIE fighter is damaged. Or R2-D2.
The novel states (on page 215 of the complete trilogy paperback):
It seems to me that the ion cannon does a good deal of damage for a weapon meant to disable ships. Am I the only one who things the EU's version of the ion cannon--i.e. the "stun setting" for starships--is a little stupid.The twin red bolts struck the enormous ship and blasted its conning tower. Explosions set off by the blast began to rock the great flying fortress, spinning it out of control.