Correct, Quality orders updating the batch disposition will affect the entire batch, which it sounds like will not work for you. You could either:
1.) Manually create an inventory block at Inventory Management -> Periodic-> Blocking for the bad inventory after passing the quality order. You could also have someone write a mod that creates this automatically based on your quality order results.
2.) Fail the quality order and generate a quarantine order, then have the quarantine order only release the good inventory.