You have to add the condition to your shipping rules by adding another trigger to the shipping rule as I outlined in my previous posts.
It is a four part process:
1) Create the checkbox on the checkout page
2) Create the hidden form element on the confirm page.
3) Add the set session value code to the confirm page
4) Add a trigger to the shipping rule so it is only applied if the session variable does not equal 1.
Look back at my previous replies for information on adding the trigger to the shipping rule.