This is possible by editing the shipping option for express shipping.  Follow the steps below to exclude the shipping cost from the total amount to discount:
  1. Fundraising>eCommerce
  2. Click Edit next to the appropriate product
  3. Skip to step 11, "Shipping Charges" and scroll down to option 7.  Uncheck the option for "Do you want to embed per-item shipping in the item price?"
  4. Click Save

If you would like to be able to add the shipping into the discount so that the purchaser doesn't have to pay anything, not even shipping, but you don't see option 7 as detailed above then do the following
 
  1. Go to Fundraising > eCommerce
  2. Select the Global eCommerce Options tab
  3. Check the box 3. Add per item shipping charge to item price
  4. Click Save